From 6f2b3f66a51b62d1c6b412f1d4cbf1a27e12fbc9 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 22 May 2015 14:35:08 -0700 Subject: [PATCH 1/7] MAINT: fixes #2024 --- qiime/workflow/downstream.py | 10 ++++++---- tests/test_workflow/test_downstream.py | 8 ++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/qiime/workflow/downstream.py b/qiime/workflow/downstream.py index 821563f986..0068e0b5d7 100644 --- a/qiime/workflow/downstream.py +++ b/qiime/workflow/downstream.py @@ -398,6 +398,7 @@ def run_jackknifed_beta_diversity(otu_table_fp, beta_diversity_metrics = ['weighted_unifrac', 'unweighted_unifrac'] # Prep the beta-diversity command + full_table_bdiv_dir = join(output_dir, 'unrarified_bdiv') try: params_str = get_params_str(params['beta_diversity']) except KeyError: @@ -406,7 +407,7 @@ def run_jackknifed_beta_diversity(otu_table_fp, params_str = '%s -t %s' % (params_str, tree_fp) # Build the beta-diversity command beta_div_cmd = 'beta_diversity.py -i %s -o %s %s' %\ - (otu_table_fp, output_dir, params_str) + (otu_table_fp, full_table_bdiv_dir, params_str) commands.append( [('Beta Diversity (%s)' % ', '.join(beta_diversity_metrics), beta_div_cmd)]) @@ -428,11 +429,12 @@ def run_jackknifed_beta_diversity(otu_table_fp, for beta_diversity_metric in beta_diversity_metrics: metric_output_dir = '%s/%s/' % (output_dir, beta_diversity_metric) distance_matrix_fp = '%s/%s_%s.txt' % \ - (output_dir, beta_diversity_metric, otu_table_basename) + (full_table_bdiv_dir, beta_diversity_metric, otu_table_basename) # Prep the hierarchical clustering command (for full distance matrix) - full_tree_fp = '%s/%s_upgma.tre' % (metric_output_dir, - otu_table_basename) + full_tree_fp = '%s/%s_%s_upgma.tre' % (full_table_bdiv_dir, + otu_table_basename, + beta_diversity_metric) try: params_str = get_params_str(params['upgma_cluster']) except KeyError: diff --git a/tests/test_workflow/test_downstream.py b/tests/test_workflow/test_downstream.py index e09b9c6737..fb48429b55 100755 --- a/tests/test_workflow/test_downstream.py +++ b/tests/test_workflow/test_downstream.py @@ -401,9 +401,9 @@ def test_run_jackknifed_beta_diversity(self): 'index.html') input_file_basename = splitext(split(self.test_data['biom'][0])[1])[0] - unweighted_unifrac_dm_fp = join(self.test_out, + unweighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', 'unweighted_unifrac_%s.txt' % input_file_basename) - weighted_unifrac_dm_fp = join(self.test_out, + weighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', 'weighted_unifrac_%s.txt' % input_file_basename) # check for expected relations between values in the unweighted unifrac @@ -460,9 +460,9 @@ def test_run_jackknifed_beta_diversity_parallel(self): 'index.html') input_file_basename = splitext(split(self.test_data['biom'][0])[1])[0] - unweighted_unifrac_dm_fp = join(self.test_out, + unweighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', 'unweighted_unifrac_%s.txt' % input_file_basename) - weighted_unifrac_dm_fp = join(self.test_out, + weighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', 'weighted_unifrac_%s.txt' % input_file_basename) # check for expected relations between values in the unweighted unifrac From 4ee1113339602542d627890e02451caa81317098 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 22 May 2015 15:03:52 -0700 Subject: [PATCH 2/7] REL/DOC: updated overview tutorial discussion --- ChangeLog.md | 3 ++- doc/tutorials/tutorial.rst | 24 ++++++++++++------------ 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 97d6020774..9a8f9d2a0f 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -12,7 +12,7 @@ Bug fixes * Forced BIOM table type to "OTU table" for all tables written with QIIME. This fixes [#1928](https://github.com/biocore/qiime/issues/1928). * The ``--similarity`` option in ``pick_otus.py`` now only accepts sequence similarity thresholds between 0.0 and 1.0 (inclusive). Previous behavior would allow values outside this range, which would cause uninformative error messages to be raised by the external tools that ``pick_otus.py`` wraps ([#1979](https://github.com/biocore/qiime/issues/1979)). * ``split_libraries_fastq.py`` now explicitly disallows ``-p 0``. This could lead to empty sequences being written to the resulting output file ([#1984](https://github.com/biocore/qiime/issues/1984)). -* Fixed issued where ``filter_samples_from_otu_table.py`` could only filter the mapping file when ``--valid_states`` was passed as the filtering method ([#2003](https://github.com/biocore/qiime/issues/2003)). +* Fixed issued where ``filter_samples_from_otu_table.py`` could only filter the mapping file when ``--valid_states`` was passed as the filtering method ([#2003](https://github.com/biocore/qiime/issues/2003)). Usability enhancements ---------------------- @@ -22,6 +22,7 @@ Usability enhancements * If ``temp_dir`` is not defined in the QIIME config file, QIIME will use the system's default temporary directory instead of assuming that ``/tmp`` is present and writeable. Note that the location of this default temporary directory [can be changed with environment variables](https://docs.python.org/2/library/tempfile.html#tempfile.tempdir) ([#1995](https://github.com/biocore/qiime/issues/1995)). * Improve error reporting from ``filter_taxa_from_otu_table.py``, ``filter_otus_from_otu_table.py``, and ``filter_samples_from_otu_table.py`` when all OTUs/samples are filtered out resulting in an empty table ([#1963](https://github.com/biocore/qiime/issues/1963)), and generally when attempting to write an empty BIOM table from QIIME. * Added ability to pass user-defined runtime limit for jobs to ``start_parallel_jobs_slurm.py``. This can be achieved by setting the ``slurm_time`` variable in ``qiime_config``, or by passing ``--time`` to ``start_parallel_jobs_slurm.py``. +* Distances matrices and UPGMA trees generated from the full (unrarified) OTU table are now stored under ``unrarified_bdiv`` in the output directory from ``jackknifed_beta_diversity.py``. That UPGMA tree is optionally used (if the user passes ``--master_tree full``). This change makes their content more explicit so they're less likely to be used by accident ([#2024](https://github.com/biocore/qiime/issues/2024)). QIIME 1.9.0 =========== diff --git a/doc/tutorials/tutorial.rst b/doc/tutorials/tutorial.rst index cabc2d62b9..9c1572ccc0 100644 --- a/doc/tutorials/tutorial.rst +++ b/doc/tutorials/tutorial.rst @@ -464,14 +464,14 @@ Jackknifed beta diversity and hierarchical clustering ----------------------------------------------------- The `jackknifed_beta_diversity.py <../scripts/jackknifed_beta_diversity.html>`_ workflow uses jackknife replicates to estimate the uncertainty in PCoA plots and hierarchical clustering of microbial communities. Many of the same concepts relevant to beta diversity and PCoA are used here. `jackknifed_beta_diversity.py <../scripts/jackknifed_beta_diversity.html>`_ performs the following steps: -1. Compute beta diversity distance matrix from full OTU table and tree, if applicable (`beta_diversity.py <../scripts/beta_diversity.html>`_) -2. Build UPGMA tree from full distance matrix (`upgma_cluster.py <../scripts/upgma_cluster.html>`_) -3. Build rarefied OTU tables (`multiple_rarefactions_even_depth.py <../scripts/multiple_rarefactions_even_depth.html>`_) -4. Compute distance matrices from rarefied OTU tables (`beta_diversity.py <../scripts/beta_diversity.html>`_) -5. Build UPGMA trees from rarefied distance matrices (`upgma_cluster.py <../scripts/upgma_cluster.html>`_) -6. Compare rarefied UPGMA trees and determine jackknife support for tree nodes (`tree_compare.py <../scripts/tree_compare.html>`_ and `consensus_tree.py <../scripts/consensus_tree.html>`_) -7. Compute PCoA on each rarefied distance matrix (`principal_coordinates.py <../scripts/principal_coordinates.html>`_) -8. Compare rarefied PCoA plots from each rarefied distance matrix (`make_emperor.py `_) +1. Compute beta diversity distance matrix from full OTU table and tree (`beta_diversity.py <../scripts/beta_diversity.html>`_). These are only used if the user passed ``--master_tree full``. +2. Build UPGMA tree from full distance matrix (`upgma_cluster.py <../scripts/upgma_cluster.html>`_). This is only used if the user passed ``--master_tree full``. +3. Build rarefied OTU tables (`multiple_rarefactions_even_depth.py <../scripts/multiple_rarefactions_even_depth.html>`_). +4. Compute distance matrices from rarefied OTU tables (`beta_diversity.py <../scripts/beta_diversity.html>`_). +5. Build UPGMA trees from rarefied distance matrices (`upgma_cluster.py <../scripts/upgma_cluster.html>`_). +6. Compare rarefied UPGMA trees and determine jackknife support for tree nodes (`tree_compare.py <../scripts/tree_compare.html>`_ and `consensus_tree.py <../scripts/consensus_tree.html>`_). +7. Compute PCoA on each rarefied distance matrix (`principal_coordinates.py <../scripts/principal_coordinates.html>`_). +8. Compare rarefied PCoA plots from each rarefied distance matrix (`make_emperor.py `_). We can run the workflow with the following command:: @@ -491,13 +491,13 @@ The output can be opened with tree viewing software, such as FigTree: :align: center :width: 700px -This tree shows the relationship among the 9 samples, and reveals that the 4 samples from the guts of fasted mice cluster together (PC.6xx, fasting data is in :file:`Fasting_Map.txt`). +This tree shows the relationship among the 9 samples, and reveals that the 4 samples from the guts of fasted mice cluster together (PC.6xx, fasting data is in :file:`Fasting_Map.txt`). The UPGMA trees resulting from this step should not be interpreted directly. Rather, they are only used in step 6 if the user passed ``--master_tree full``. The default (``--master_tree consensus``) will result in a more biologically meaningful result, so these are provided only as a legacy option. .. _jacksupport: Steps 3, 4, and 5. Perform jackknifing support ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To measure the robustness of our results to sequencing effort, we perform a jackknifing analysis, wherein a smaller number of sequences are chosen at random from each sample, and the resulting UPGMA tree from this subset of data is compared with the tree representing the entire data set. This process is repeated with many random subsets of data, and the tree nodes which prove more consistent across jackknifed datasets are deemed more robust. +To measure the robustness of our results to sequencing depth, we perform a jackknifing analysis, wherein a smaller number of sequences are chosen at random from each sample, and the resulting UPGMA tree from this subset of data is compared with the tree representing the entire data set. This process is repeated with many random subsets of data, and the tree nodes which prove more consistent across jackknifed datasets are deemed more robust. First, the jackknifed OTU tables must be generated by subsampling the full data set. In this tutorial, each sample contains between 146 and 150 sequences, as shown with `biom summarize-table`__. @@ -513,9 +513,9 @@ The workflow then computes a distance matrix for each jackknifed dataset, which Step 6. Compare rarefied UPGMA trees and determine jackknife support for tree nodes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -UPGMA clustering of the 10 distance matrices results in 10 hierarchical clusters of the 9 mouse microbial communities, with each hierarchical cluster being based on a random subsample of the available sequence data. +UPGMA clustering of the 10 distance matrices results in 10 hierarchical clusterings (or UPGMA trees) of the 9 mouse microbial communities, with each UPGMA tree being based on a random subsample of the available sequence data. -This step of the workflow compares the UPGMA clustering based on the full data set with the jackknifed UPGMA results. Three files are written to :file:`jack/unweighted_unifrac/upgma_cmp/` and :file:`jack/weighted_unifrac/upgma_cmp/`: +This step of the workflow compares each UPGMA tree to a consensus of those trees. Three files are written to :file:`jack/unweighted_unifrac/upgma_cmp/` and :file:`jack/weighted_unifrac/upgma_cmp/`: * :file:`master_tree.tre`, which is identical to :file:`jackknife_named_nodes.tre` but each internal node of the UPGMA clustering is assigned a unique name * :file:`jackknife_named_nodes.tre` From f4b3463fd4a84ec1ce7c5b5df7b0ad1d9dd1a052 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 22 May 2015 15:28:36 -0700 Subject: [PATCH 3/7] REL: updated version for 1.9.1 release --- ChangeLog.md | 4 +-- doc/conf.py | 4 +-- doc/scripts/align_seqs.rst | 2 +- doc/scripts/assign_taxonomy.rst | 4 +-- doc/scripts/collapse_samples.rst | 2 +- doc/scripts/denoiser_worker.rst | 2 +- doc/scripts/exclude_seqs_by_blast.rst | 2 +- doc/scripts/filter_fasta.rst | 16 ++++++------ doc/scripts/jackknifed_beta_diversity.rst | 6 ++--- doc/scripts/normalize_table.rst | 25 +++++++++++++++---- doc/scripts/parallel_align_seqs_pynast.rst | 2 +- .../parallel_assign_taxonomy_blast.rst | 4 +-- doc/scripts/parallel_assign_taxonomy_rdp.rst | 6 ++--- .../parallel_assign_taxonomy_uclust.rst | 4 +-- .../parallel_identify_chimeric_seqs.rst | 2 +- doc/scripts/pick_closed_reference_otus.rst | 4 +-- doc/scripts/pick_open_reference_otus.rst | 2 +- doc/scripts/pick_otus.rst | 4 +-- doc/scripts/split_libraries_fastq.rst | 8 +++--- doc/scripts/start_parallel_jobs_slurm.rst | 2 ++ doc/scripts/summarize_taxa.rst | 2 +- qiime/__init__.py | 2 +- qiime/add_alpha_to_mapping_file.py | 2 +- qiime/add_qiime_labels.py | 2 +- qiime/adjust_seq_orientation.py | 2 +- qiime/align_seqs.py | 2 +- qiime/alpha_diversity.py | 2 +- qiime/assign_taxonomy.py | 2 +- qiime/barcode.py | 2 +- qiime/beta_diversity.py | 2 +- qiime/beta_metrics.py | 2 +- qiime/biplots.py | 2 +- qiime/categorized_dist_scatterplot.py | 2 +- qiime/check_id_map.py | 2 +- qiime/clean_raxml_parsimony_tree.py | 2 +- qiime/cluster_quality.py | 2 +- qiime/collate_alpha.py | 2 +- qiime/colors.py | 2 +- qiime/compare_alpha_diversity.py | 2 +- qiime/compare_categories.py | 2 +- qiime/compare_distance_matrices.py | 2 +- qiime/compare_taxa_summaries.py | 2 +- qiime/compare_trajectories.py | 2 +- qiime/compute_taxonomy_ratios.py | 2 +- qiime/convert_fastaqual_fastq.py | 2 +- qiime/core_microbiome.py | 2 +- qiime/demultiplex_fasta.py | 2 +- qiime/denoise_wrapper.py | 2 +- qiime/denoiser/__init__.py | 2 +- qiime/denoiser/cluster_utils.py | 2 +- qiime/denoiser/denoise_postprocess.py | 2 +- qiime/denoiser/denoise_worker.py | 2 +- qiime/denoiser/flowgram_clustering.py | 2 +- qiime/denoiser/flowgram_filter.py | 2 +- qiime/denoiser/make_cluster_jobs.py | 2 +- qiime/denoiser/preprocess.py | 2 +- qiime/denoiser/utils.py | 2 +- qiime/detrend.py | 2 +- qiime/differential_abundance.py | 2 +- qiime/distance_matrix_from_mapping.py | 2 +- qiime/estimate_observation_richness.py | 2 +- qiime/exclude_seqs_by_blast.py | 2 +- qiime/extract_barcodes.py | 2 +- qiime/filter.py | 2 +- qiime/filter_alignment.py | 2 +- qiime/filter_otus_by_sample.py | 2 +- qiime/format.py | 2 +- qiime/golay.py | 2 +- qiime/group.py | 2 +- qiime/hamming.py | 2 +- qiime/hierarchical_cluster.py | 2 +- qiime/identify_chimeric_seqs.py | 2 +- qiime/join_paired_ends.py | 2 +- qiime/make_2d_plots.py | 2 +- qiime/make_bipartite_network.py | 2 +- qiime/make_bootstrapped_tree.py | 2 +- qiime/make_distance_boxplots.py | 2 +- qiime/make_fastq.py | 2 +- qiime/make_library_id_lists.py | 2 +- qiime/make_otu_heatmap.py | 2 +- qiime/make_otu_network.py | 2 +- qiime/make_otu_table.py | 2 +- qiime/make_per_library_sff.py | 2 +- qiime/make_phylogeny.py | 2 +- qiime/make_rarefaction_plots.py | 2 +- qiime/map_reads_to_reference.py | 2 +- qiime/nmds.py | 2 +- qiime/normalize_table.py | 2 +- qiime/otu_significance.py | 2 +- qiime/parallel/__init__.py | 2 +- qiime/parallel/align_seqs.py | 2 +- qiime/parallel/alpha_diversity.py | 2 +- qiime/parallel/assign_taxonomy.py | 2 +- qiime/parallel/beta_diversity.py | 2 +- qiime/parallel/blast.py | 2 +- qiime/parallel/identify_chimeric_seqs.py | 2 +- qiime/parallel/map_reads_to_reference.py | 2 +- qiime/parallel/merge_otus.py | 2 +- qiime/parallel/multiple_rarefactions.py | 2 +- qiime/parallel/pick_otus.py | 2 +- qiime/parallel/poller.py | 2 +- qiime/parallel/util.py | 2 +- qiime/parse.py | 2 +- qiime/pick_otus.py | 2 +- qiime/pick_rep_set.py | 2 +- qiime/plot_rank_abundance_graph.py | 2 +- qiime/plot_semivariogram.py | 2 +- qiime/plot_taxa_summary.py | 2 +- qiime/principal_coordinates.py | 2 +- qiime/process_sff.py | 2 +- qiime/pycogent_backports/__init__.py | 2 +- qiime/quality_scores_plot.py | 2 +- qiime/rarefaction.py | 2 +- qiime/relatedness_library.py | 2 +- qiime/remote.py | 2 +- qiime/shared_phylotypes.py | 2 +- qiime/simsam.py | 2 +- qiime/sort.py | 2 +- qiime/split.py | 2 +- qiime/split_libraries.py | 2 +- qiime/split_libraries_fastq.py | 2 +- qiime/split_libraries_lea_seq.py | 2 +- qiime/stats.py | 2 +- qiime/summarize_taxa.py | 2 +- qiime/supervised_learning.py | 2 +- qiime/support_files/R/util.r | 2 +- qiime/support_files/js/otu_count_display.js | 2 +- .../test_js/test_otu_count_display.html | 2 +- qiime/test.py | 2 +- qiime/transform_coordinate_matrices.py | 2 +- qiime/tree_compare.py | 2 +- qiime/trim_sff_primers.py | 2 +- qiime/truncate_fasta_qual_files.py | 2 +- qiime/truncate_reverse_primer.py | 2 +- qiime/util.py | 2 +- qiime/validate_demultiplexed_fasta.py | 2 +- qiime/workflow/__init__.py | 2 +- qiime/workflow/ampliconnoise.py | 2 +- qiime/workflow/core_diversity_analyses.py | 2 +- qiime/workflow/downstream.py | 2 +- qiime/workflow/pick_open_reference_otus.py | 2 +- qiime/workflow/preprocess.py | 2 +- qiime/workflow/upstream.py | 2 +- qiime/workflow/util.py | 2 +- scripts/add_alpha_to_mapping_file.py | 2 +- scripts/add_qiime_labels.py | 2 +- scripts/adjust_seq_orientation.py | 2 +- scripts/align_seqs.py | 2 +- scripts/alpha_diversity.py | 2 +- scripts/alpha_rarefaction.py | 2 +- scripts/ampliconnoise.py | 2 +- scripts/assign_taxonomy.py | 2 +- scripts/beta_diversity.py | 2 +- scripts/beta_diversity_through_plots.py | 2 +- scripts/beta_significance.py | 2 +- scripts/blast_wrapper.py | 2 +- scripts/categorized_dist_scatterplot.py | 2 +- scripts/check_id_map.py | 2 +- scripts/clean_raxml_parsimony_tree.py | 2 +- scripts/cluster_quality.py | 2 +- scripts/collapse_samples.py | 2 +- scripts/collate_alpha.py | 2 +- scripts/compare_alpha_diversity.py | 2 +- scripts/compare_categories.py | 2 +- scripts/compare_distance_matrices.py | 2 +- scripts/compare_taxa_summaries.py | 2 +- scripts/compare_trajectories.py | 2 +- scripts/compute_core_microbiome.py | 2 +- scripts/compute_taxonomy_ratios.py | 2 +- scripts/conditional_uncovered_probability.py | 2 +- scripts/consensus_tree.py | 2 +- scripts/convert_fastaqual_fastq.py | 2 +- ...ert_unifrac_sample_mapping_to_otu_table.py | 2 +- scripts/core_diversity_analyses.py | 2 +- scripts/count_seqs.py | 2 +- scripts/demultiplex_fasta.py | 2 +- scripts/denoise_wrapper.py | 2 +- scripts/denoiser.py | 2 +- scripts/denoiser_preprocess.py | 2 +- scripts/denoiser_worker.py | 2 +- scripts/detrend.py | 2 +- scripts/differential_abundance.py | 2 +- scripts/dissimilarity_mtx_stats.py | 2 +- scripts/distance_matrix_from_mapping.py | 2 +- scripts/estimate_observation_richness.py | 2 +- scripts/exclude_seqs_by_blast.py | 2 +- scripts/extract_barcodes.py | 2 +- .../extract_reads_from_interleaved_file.py | 2 +- scripts/extract_seqs_by_sample_id.py | 2 +- scripts/filter_alignment.py | 2 +- scripts/filter_distance_matrix.py | 2 +- scripts/filter_fasta.py | 2 +- scripts/filter_otus_by_sample.py | 2 +- scripts/filter_otus_from_otu_table.py | 2 +- scripts/filter_samples_from_otu_table.py | 2 +- scripts/filter_taxa_from_otu_table.py | 2 +- scripts/filter_tree.py | 2 +- scripts/fix_arb_fasta.py | 2 +- scripts/group_significance.py | 2 +- scripts/identify_chimeric_seqs.py | 2 +- scripts/identify_missing_files.py | 2 +- scripts/identify_paired_differences.py | 2 +- scripts/inflate_denoiser_output.py | 2 +- scripts/jackknifed_beta_diversity.py | 2 +- scripts/join_paired_ends.py | 2 +- scripts/load_remote_mapping_file.py | 2 +- scripts/make_2d_plots.py | 2 +- scripts/make_bipartite_network.py | 2 +- scripts/make_bootstrapped_tree.py | 2 +- scripts/make_distance_boxplots.py | 2 +- scripts/make_distance_comparison_plots.py | 2 +- scripts/make_fastq.py | 2 +- scripts/make_library_id_lists.py | 2 +- scripts/make_otu_heatmap.py | 2 +- scripts/make_otu_network.py | 2 +- scripts/make_otu_table.py | 2 +- scripts/make_per_library_sff.py | 2 +- scripts/make_phylogeny.py | 2 +- scripts/make_prefs_file.py | 2 +- scripts/make_qiime_py_file.py | 4 +-- scripts/make_rarefaction_plots.py | 2 +- scripts/make_tep.py | 2 +- scripts/map_reads_to_reference.py | 2 +- scripts/merge_mapping_files.py | 2 +- scripts/merge_otu_maps.py | 2 +- scripts/merge_otu_tables.py | 2 +- scripts/multiple_extract_barcodes.py | 2 +- scripts/multiple_join_paired_ends.py | 2 +- scripts/multiple_rarefactions.py | 2 +- scripts/multiple_rarefactions_even_depth.py | 2 +- scripts/multiple_split_libraries_fastq.py | 2 +- scripts/neighbor_joining.py | 2 +- scripts/nmds.py | 2 +- scripts/normalize_table.py | 2 +- scripts/observation_metadata_correlation.py | 2 +- scripts/otu_category_significance.py | 2 +- scripts/parallel_align_seqs_pynast.py | 2 +- scripts/parallel_alpha_diversity.py | 2 +- scripts/parallel_assign_taxonomy_blast.py | 2 +- scripts/parallel_assign_taxonomy_rdp.py | 2 +- scripts/parallel_assign_taxonomy_uclust.py | 2 +- scripts/parallel_beta_diversity.py | 2 +- scripts/parallel_blast.py | 2 +- scripts/parallel_identify_chimeric_seqs.py | 2 +- scripts/parallel_map_reads_to_reference.py | 2 +- scripts/parallel_merge_otu_tables.py | 2 +- scripts/parallel_multiple_rarefactions.py | 2 +- scripts/parallel_pick_otus_blast.py | 2 +- scripts/parallel_pick_otus_sortmerna.py | 2 +- scripts/parallel_pick_otus_trie.py | 2 +- scripts/parallel_pick_otus_uclust_ref.py | 2 +- scripts/parallel_pick_otus_usearch61_ref.py | 2 +- scripts/pick_closed_reference_otus.py | 2 +- scripts/pick_de_novo_otus.py | 2 +- scripts/pick_open_reference_otus.py | 2 +- scripts/pick_otus.py | 2 +- scripts/pick_rep_set.py | 2 +- scripts/plot_rank_abundance_graph.py | 2 +- scripts/plot_semivariogram.py | 2 +- scripts/plot_taxa_summary.py | 2 +- scripts/poller.py | 2 +- scripts/principal_coordinates.py | 2 +- scripts/print_metadata_stats.py | 2 +- scripts/print_qiime_config.py | 2 +- scripts/process_iseq.py | 2 +- scripts/process_qseq.py | 2 +- scripts/process_sff.py | 2 +- scripts/quality_scores_plot.py | 2 +- scripts/relatedness.py | 2 +- scripts/shared_phylotypes.py | 2 +- scripts/simsam.py | 2 +- scripts/single_rarefaction.py | 2 +- scripts/sort_otu_table.py | 2 +- scripts/split_libraries.py | 2 +- scripts/split_libraries_fastq.py | 2 +- scripts/split_libraries_lea_seq.py | 2 +- scripts/split_otu_table.py | 2 +- scripts/split_otu_table_by_taxonomy.py | 2 +- scripts/split_sequence_file_on_sample_ids.py | 2 +- scripts/start_parallel_jobs.py | 2 +- scripts/start_parallel_jobs_sc.py | 2 +- scripts/start_parallel_jobs_slurm.py | 2 +- scripts/start_parallel_jobs_torque.py | 2 +- scripts/subsample_fasta.py | 2 +- scripts/summarize_taxa.py | 2 +- scripts/summarize_taxa_through_plots.py | 2 +- scripts/supervised_learning.py | 2 +- scripts/transform_coordinate_matrices.py | 2 +- scripts/tree_compare.py | 2 +- scripts/trflp_file_to_otu_table.py | 2 +- scripts/trim_sff_primers.py | 2 +- scripts/truncate_fasta_qual_files.py | 2 +- scripts/truncate_reverse_primer.py | 2 +- scripts/unweight_fasta.py | 2 +- scripts/upgma_cluster.py | 2 +- scripts/validate_demultiplexed_fasta.py | 2 +- scripts/validate_mapping_file.py | 2 +- setup.py | 2 +- tests/__init__.py | 2 +- tests/all_tests.py | 2 +- tests/test_add_alpha_to_mapping_file.py | 2 +- tests/test_add_qiime_labels.py | 2 +- tests/test_adjust_seq_orientation.py | 2 +- tests/test_align_seqs.py | 2 +- tests/test_alpha_diversity.py | 2 +- tests/test_assign_taxonomy.py | 2 +- tests/test_barcode.py | 2 +- tests/test_beta_diversity.py | 2 +- tests/test_beta_metrics.py | 2 +- tests/test_biplots.py | 2 +- tests/test_categorized_dist_scatterplot.py | 2 +- tests/test_clean_raxml_parsimony_tree.py | 2 +- tests/test_cluster_quality.py | 2 +- tests/test_collate_alpha.py | 2 +- tests/test_colors.py | 2 +- tests/test_compare_alpha_diversity.py | 2 +- tests/test_compare_categories.py | 2 +- tests/test_compare_distance_matrices.py | 2 +- tests/test_compare_taxa_summaries.py | 2 +- tests/test_compare_trajectories.py | 2 +- tests/test_compute_taxonomy_ratios.py | 2 +- tests/test_convert_fastaqual_fastq.py | 2 +- tests/test_core_microbiome.py | 2 +- tests/test_demultiplex_fasta.py | 2 +- tests/test_denoise_wrapper.py | 2 +- tests/test_denoiser/test_cluster_util.py | 2 +- .../test_denoiser/test_denoise_postprocess.py | 2 +- tests/test_denoiser/test_denoiser.py | 2 +- .../test_denoiser/test_flowgram_clustering.py | 2 +- tests/test_denoiser/test_flowgram_filter.py | 2 +- tests/test_denoiser/test_make_cluster_jobs.py | 2 +- tests/test_denoiser/test_preprocess.py | 2 +- tests/test_denoiser/test_settings.py | 2 +- tests/test_denoiser/test_utils.py | 2 +- tests/test_detrend.py | 2 +- tests/test_differential_abundance.py | 2 +- tests/test_distance_matrix_from_mapping.py | 2 +- tests/test_estimate_observation_richness.py | 2 +- tests/test_exclude_seqs_by_blast.py | 2 +- tests/test_extract_barcodes.py | 2 +- tests/test_filter.py | 2 +- tests/test_filter_alignment.py | 2 +- tests/test_filter_otus_by_sample.py | 2 +- tests/test_format.py | 2 +- tests/test_golay.py | 2 +- tests/test_group.py | 2 +- tests/test_hamming.py | 2 +- tests/test_hierarchical_cluster.py | 2 +- tests/test_identify_chimeric_seqs.py | 2 +- tests/test_join_paired_ends.py | 2 +- tests/test_make_2d_plots.py | 2 +- tests/test_make_bipartite_network.py | 2 +- tests/test_make_bootstrapped_tree.py | 2 +- tests/test_make_distance_boxplots.py | 2 +- tests/test_make_fastq.py | 2 +- tests/test_make_library_id_lists.py | 2 +- tests/test_make_otu_heatmap.py | 2 +- tests/test_make_otu_network.py | 2 +- tests/test_make_otu_table.py | 2 +- tests/test_make_per_library_sff.py | 2 +- tests/test_make_phylogeny.py | 2 +- tests/test_make_rarefaction_plots.py | 2 +- tests/test_map_reads_to_reference.py | 2 +- tests/test_normalize_table.py | 2 +- tests/test_otu_significance.py | 2 +- tests/test_parallel/test_align_seqs.py | 2 +- tests/test_parallel/test_alpha_diversity.py | 2 +- tests/test_parallel/test_assign_taxonomy.py | 2 +- tests/test_parallel/test_beta_diversity.py | 2 +- tests/test_parallel/test_blast.py | 2 +- .../test_identify_chimeric_seqs.py | 2 +- .../test_map_reads_to_reference.py | 2 +- tests/test_parallel/test_merge_otus.py | 2 +- .../test_multiple_rarefactions.py | 2 +- tests/test_parallel/test_pick_otus.py | 2 +- tests/test_parallel/test_util.py | 2 +- tests/test_parse.py | 2 +- tests/test_pick_otus.py | 2 +- tests/test_pick_rep_set.py | 2 +- tests/test_plot_rank_abundance_graph.py | 2 +- tests/test_plot_semivariogram.py | 2 +- tests/test_plot_taxa_summary.py | 2 +- tests/test_principal_coordinates.py | 2 +- tests/test_process_sff.py | 2 +- tests/test_quality_scores_plot.py | 2 +- tests/test_rarefaction.py | 2 +- tests/test_relatedness.py | 2 +- tests/test_remote.py | 2 +- tests/test_shared_phylotypes.py | 2 +- tests/test_simsam.py | 2 +- tests/test_sort.py | 2 +- tests/test_split.py | 2 +- tests/test_split_libraries.py | 2 +- tests/test_split_libraries_fastq.py | 2 +- tests/test_split_libraries_lea_seq.py | 2 +- tests/test_stats.py | 2 +- tests/test_summarize_taxa.py | 2 +- tests/test_supervised_learning.py | 2 +- tests/test_transform_coordinate_matrices.py | 2 +- tests/test_tree_compare.py | 2 +- tests/test_trim_sff_primers.py | 2 +- tests/test_truncate_fasta_qual_files.py | 2 +- tests/test_truncate_reverse_primer.py | 2 +- tests/test_util.py | 2 +- tests/test_validate_demultiplexed_fasta.py | 2 +- tests/test_validate_mapping_file.py | 2 +- tests/test_workflow/test_ampliconnoise.py | 2 +- .../test_core_diversity_analyses.py | 2 +- tests/test_workflow/test_downstream.py | 2 +- .../test_pick_open_reference_otus.py | 2 +- tests/test_workflow/test_preprocess.py | 2 +- tests/test_workflow/test_upstream.py | 2 +- tests/test_workflow/test_util.py | 2 +- 413 files changed, 455 insertions(+), 438 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 9e7513c2ac..d146dcf84a 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,5 +1,5 @@ -QIIME 1.9.0-dev -=============== +QIIME 1.9.1 +=========== Bug fixes --------- diff --git a/doc/conf.py b/doc/conf.py index b67bfb1b19..94a8875251 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -46,9 +46,9 @@ # built documents. # # The short X.Y version. -version = '1.9.0-dev' +version = '1.9.1' # The full version, including alpha/beta/rc tags. -release = '1.9.0-dev' +release = '1.9.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/doc/scripts/align_seqs.rst b/doc/scripts/align_seqs.rst index e39c192f5b..f8b92dbb5b 100644 --- a/doc/scripts/align_seqs.rst +++ b/doc/scripts/align_seqs.rst @@ -37,7 +37,7 @@ This script aligns the sequences in a FASTA file to each other or to a template -a, `-`-pairwise_alignment_method Method for performing pairwise alignment in PyNAST. Valid choices are muscle, pair_hmm, clustal, blast, uclust, mafft [default: uclust] -t, `-`-template_fp - Filepath for template alignment [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.fasta] + Filepath for template alignment [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/`85_otus.py <./85_otus.html>`_nast.fasta] -e, `-`-min_length Minimum sequence length to include in alignment [default: 75% of the median input sequence length] -p, `-`-min_percent_id diff --git a/doc/scripts/assign_taxonomy.rst b/doc/scripts/assign_taxonomy.rst index 4ecbed54a8..eddd7183e6 100644 --- a/doc/scripts/assign_taxonomy.rst +++ b/doc/scripts/assign_taxonomy.rst @@ -33,9 +33,9 @@ Reference data sets and id-to-taxonomy maps for 16S rRNA sequences can be found **[OPTIONAL]** -t, `-`-id_to_taxonomy_fp - Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep. [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] + Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep. [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] -r, `-`-reference_seqs_fp - Path to reference sequences. For assignment with blast, these are used to generate a blast database. For assignment with rdp, they are used as training sequences for the classifier. [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] + Path to reference sequences. For assignment with blast, these are used to generate a blast database. For assignment with rdp, they are used as training sequences for the classifier. [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] -p, `-`-training_data_properties_fp Path to ".properties" file in pre-compiled training data for the RDP Classifier. This option is overridden by the -t and -r options. [default: None] `-`-read_1_seqs_fp diff --git a/doc/scripts/collapse_samples.rst b/doc/scripts/collapse_samples.rst index 806d019b20..0b6f4b541b 100644 --- a/doc/scripts/collapse_samples.rst +++ b/doc/scripts/collapse_samples.rst @@ -33,7 +33,7 @@ Collapse samples in a BIOM table and mapping file. Values in the BIOM table are **[OPTIONAL]** `-`-collapse_mode - The mechanism for collapsing counts within groups; valid options are: mean, sum, random, median, first + The mechanism for collapsing counts within groups; valid options are: mean, sum, random, median, first. [default: sum] `-`-normalize Normalize observation counts to relative abundances, so the counts within each sample sum to 1.0. [default: False] diff --git a/doc/scripts/denoiser_worker.rst b/doc/scripts/denoiser_worker.rst index b2547319f4..b82b5a776b 100644 --- a/doc/scripts/denoiser_worker.rst +++ b/doc/scripts/denoiser_worker.rst @@ -32,7 +32,7 @@ A worker waits for data and does flowgram alignments once it gets it. **[OPTIONAL]** -e, `-`-error_profile - Path to error profile [DEFAULT: /Users/jairideout/dev/qiime/qiime/support_files/denoiser/Data/FLX_error_profile.dat] + Path to error profile [DEFAULT: /Users/caporaso/Dropbox/code/Qiime/qiime/support_files/denoiser/Data/FLX_error_profile.dat] -c, `-`-counter Round counter to start this worker with [default: 0] diff --git a/doc/scripts/exclude_seqs_by_blast.rst b/doc/scripts/exclude_seqs_by_blast.rst index 6abe5a8281..3cac3c884f 100644 --- a/doc/scripts/exclude_seqs_by_blast.rst +++ b/doc/scripts/exclude_seqs_by_blast.rst @@ -48,7 +48,7 @@ WARNING: You cannot use this script if there are spaces in the path to the datab `-`-blastmatroot Path to a folder containing blast matrices [default: None]. `-`-working_dir - Working dir for BLAST [default: /tmp/]. + Working dir for BLAST [default: /Users/caporaso/temp/]. -m, `-`-max_hits Max hits parameter for BLAST. CAUTION: Because filtering on alignment percentage occurs after BLAST, a max hits value of 1 in combination with an alignment percent filter could miss valid contaminants. [default: 100] -w, `-`-word_size diff --git a/doc/scripts/filter_fasta.rst b/doc/scripts/filter_fasta.rst index 6cee6c809f..06d8a04ab0 100644 --- a/doc/scripts/filter_fasta.rst +++ b/doc/scripts/filter_fasta.rst @@ -27,23 +27,23 @@ **[OPTIONAL]** -m, `-`-otu_map - An OTU map where sequences ids are those which should be retained + An OTU map where sequences ids are those which should be retained. -s, `-`-seq_id_fp - A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained + A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained. -b, `-`-biom_fp - A biom file where otu identifiers should be retained + A biom file where otu identifiers should be retained. -a, `-`-subject_fasta_fp A fasta file where the seq ids should be retained. -p, `-`-seq_id_prefix - Keep seqs where seq_id starts with this prefix + Keep seqs where seq_id starts with this prefix. `-`-sample_id_fp - Keep seqs where seq_id starts with a sample id listed in this file + Keep seqs where seq_id starts with a sample id listed in this file. Must be newline delimited and may not contain a header. -n, `-`-negate - Discard passed seq ids rather than keep passed seq ids [default: False] + Discard passed seq ids rather than keep passed seq ids. [default: False] `-`-mapping_fp - Mapping file path (for use with --valid_states) [default: None] + Mapping file path (for use with --valid_states). [default: None] `-`-valid_states - Description of sample ids to retain (for use with --mapping_fp) [default: None] + Description of sample ids to retain (for use with --mapping_fp). [default: None] **Output:** diff --git a/doc/scripts/jackknifed_beta_diversity.rst b/doc/scripts/jackknifed_beta_diversity.rst index 8ca4aa7532..96d0943b5b 100644 --- a/doc/scripts/jackknifed_beta_diversity.rst +++ b/doc/scripts/jackknifed_beta_diversity.rst @@ -2,7 +2,7 @@ .. index:: jackknifed_beta_diversity.py -*jackknifed_beta_diversity.py* -- A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D PCoA plots. +*jackknifed_beta_diversity.py* -- A workflow script for performing jackknifed UPGMA clustering and building jackknifed Emperor PCoA plots. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ **Description:** @@ -48,12 +48,12 @@ To directly measure the robustness of individual UPGMA clusters and clusters in **Output:** -This scripts results in several distance matrices (from `beta_diversity.py <./beta_diversity.html>`_), several rarified OTU tables (from `multiple_rarefactions_even_depth.py <./multiple_rarefactions_even_depth.html>`_), several UPGMA trees (from `upgma_cluster.py <./upgma_cluster.html>`_), a supporting file and newick tree with support values (from `tree_compare.py <./tree_compare.html>`_), and 2D and 3D PCoA plots. +This scripts results in several distance matrices (from `beta_diversity.py <./beta_diversity.html>`_), several rarified OTU tables (from `multiple_rarefactions_even_depth.py <./multiple_rarefactions_even_depth.html>`_), several UPGMA trees (from `upgma_cluster.py <./upgma_cluster.html>`_), a supporting file and newick tree with support values (from `tree_compare.py <./tree_compare.html>`_), and Emperor PCoA plots. **Example:** -These steps are performed by the following command: Compute beta diversity distance matrix from otu table (and tree, if applicable); build rarefied OTU tables by evenly sampling to the specified depth (-e); build UPGMA tree from full distance matrix; compute distance matrics for rarefied OTU tables; build UPGMA trees from rarefied OTU table distance matrices; build a consensus tree from the rarefied UPGMA trees; compare rarefied OTU table distance matrix UPGMA trees to either (full or consensus) tree for jackknife support of tree nodes; perform principal coordinates analysis on distance matrices generated from rarefied OTU tables; generate 2D and 3D PCoA plots with jackknifed support. +These steps are performed by the following command: Compute beta diversity distance matrix from otu table (and tree, if applicable); build rarefied OTU tables by evenly sampling to the specified depth (-e); build UPGMA tree from full distance matrix; compute distance matrics for rarefied OTU tables; build UPGMA trees from rarefied OTU table distance matrices; build a consensus tree from the rarefied UPGMA trees; compare rarefied OTU table distance matrix UPGMA trees to either (full or consensus) tree for jackknife support of tree nodes; perform principal coordinates analysis on distance matrices generated from rarefied OTU tables; generate Emperor PCoA plots with jackknifed support. diff --git a/doc/scripts/normalize_table.rst b/doc/scripts/normalize_table.rst index 1172573d9b..97c618d4cc 100644 --- a/doc/scripts/normalize_table.rst +++ b/doc/scripts/normalize_table.rst @@ -27,22 +27,37 @@ it be 0.01 instead of 1?), for more information read Costea, P. et al. (2014) DESeq/DESeq2 can also have a very slow runtime, especially for larger datasets. In this script, we implement DESeq2's variance stabilization technique. If you do use these alternatives to rarefying, we would recommend metagenomeSeq's CSS (cumulative sum -scaling) transformation for those metrics that are abundance-based. It is not +scaling) transformation for those metrics that are abundance-based. It is not recommended to use these new methods with presence/absence metrics, for example -binary Jaccard or unweighted UniFrac. +binary Jaccard or unweighted UniFrac. For more on metagenomeSeq's CSS, please see Paulson, JN, et al. 'Differential abundance analysis for microbial marker-gene surveys' Nature Methods 2013. For DESeq please see Anders S, Huber W. 'Differential expression analysis for sequence -count data.' Genome Biology 2010. For DESeq2 please read Love, MI et al. -'Moderated estimation of fold change and dispersion for RNA-Seq data +count data.' Genome Biology 2010. For DESeq2 please read Love, MI et al. +'Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2,' Genome Biology 2014. If you use these methods, please CITE the appropriate reference as well as QIIME. For any of these methods, clustering by sequence depth MUST BE CHECKED FOR as a confounding variable, e.g. by coloring by sequences/sample on a PCoA plot and testing for correlations between -taxa abundances and sequencing depth with e.g. adonis in `compare_categories.py <./compare_categories.html>`_, +taxa abundances and sequencing depth with e.g. adonis in `compare_categories.py <./compare_categories.html>`_, or `observation_metadata_correlation.py <./observation_metadata_correlation.html>`_. +Note: If the input BIOM table contains observation metadata (e.g., taxonomy +metadata for each OTU), this metadata will not be included in the output +normalized BIOM table when using DESeq2. When using CSS the taxonomy metadata +will be included in the output normalized table but it may not be in the same +format as the input table (e.g., "NA" will be added for missing taxonomic +levels). This discrepancy occurs because the underlying R packages used to +perform the normalization store taxonomy metadata in a different format. + +As a workaround, the "biom add-metadata" command can be used to add the +original observation metadata to the output normalized table if desired. For +example, to include the original taxonomy metadata on the output normalized +table, "biom add-metadata" can be used with the representative sequence +taxonomic assignment file output by `assign_taxonomy.py <./assign_taxonomy.html>`_. + + **Usage:** :file:`normalize_table.py [options]` diff --git a/doc/scripts/parallel_align_seqs_pynast.rst b/doc/scripts/parallel_align_seqs_pynast.rst index fb8f2d9767..09ce75c536 100644 --- a/doc/scripts/parallel_align_seqs_pynast.rst +++ b/doc/scripts/parallel_align_seqs_pynast.rst @@ -27,7 +27,7 @@ A wrapper for the `align_seqs.py <./align_seqs.html>`_ PyNAST option, intended t **[OPTIONAL]** -t, `-`-template_fp - Filepath for template alignment [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.fasta] + Filepath for template alignment [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/`85_otus.py <./85_otus.html>`_nast.fasta] -a, `-`-pairwise_alignment_method Method to use for pairwise alignments [default: uclust] -d, `-`-blast_db diff --git a/doc/scripts/parallel_assign_taxonomy_blast.rst b/doc/scripts/parallel_assign_taxonomy_blast.rst index 320e468949..477d5d709f 100644 --- a/doc/scripts/parallel_assign_taxonomy_blast.rst +++ b/doc/scripts/parallel_assign_taxonomy_blast.rst @@ -27,7 +27,7 @@ This script performs like the `assign_taxonomy.py <./assign_taxonomy.html>`_ scr **[OPTIONAL]** -r, `-`-reference_seqs_fp - Ref seqs to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] + Ref seqs to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] -b, `-`-blast_db Database to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: None] -e, `-`-e_value @@ -51,7 +51,7 @@ This script performs like the `assign_taxonomy.py <./assign_taxonomy.html>`_ scr -Z, `-`-seconds_to_sleep Number of seconds to sleep between checks for run completion when polling runs [default: 1] -t, `-`-id_to_taxonomy_fp - Full path to id_to_taxonomy mapping file [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] + Full path to id_to_taxonomy mapping file [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] **Output:** diff --git a/doc/scripts/parallel_assign_taxonomy_rdp.rst b/doc/scripts/parallel_assign_taxonomy_rdp.rst index bb44bf6166..37e5b7f64a 100644 --- a/doc/scripts/parallel_assign_taxonomy_rdp.rst +++ b/doc/scripts/parallel_assign_taxonomy_rdp.rst @@ -27,13 +27,13 @@ This script performs like the `assign_taxonomy.py <./assign_taxonomy.html>`_ scr **[OPTIONAL]** `-`-rdp_classifier_fp - Full path to rdp classifier jar file [default: None] + Full path to rdp classifier jar file [default: /Users/caporaso/Dropbox/bin/rdp_classifier_2.2/rdp_classifier-2.2.jar] -c, `-`-confidence Minimum confidence to record an assignment [default: 0.5] -t, `-`-id_to_taxonomy_fp - Full path to id_to_taxonomy mapping file [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] + Full path to id_to_taxonomy mapping file [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] -r, `-`-reference_seqs_fp - Ref seqs to rdp against. [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] + Ref seqs to rdp against. [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] `-`-rdp_max_memory Maximum memory allocation, in MB, for Java virtual machine when using the rdp method. Increase for large training sets [default: 4000] -O, `-`-jobs_to_start diff --git a/doc/scripts/parallel_assign_taxonomy_uclust.rst b/doc/scripts/parallel_assign_taxonomy_uclust.rst index 50839cd230..35a14bb4ed 100644 --- a/doc/scripts/parallel_assign_taxonomy_uclust.rst +++ b/doc/scripts/parallel_assign_taxonomy_uclust.rst @@ -27,9 +27,9 @@ This script performs like the `assign_taxonomy.py <./assign_taxonomy.html>`_ scr **[OPTIONAL]** -t, `-`-id_to_taxonomy_fp - Full path to id_to_taxonomy mapping file [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] + Full path to id_to_taxonomy mapping file [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] -r, `-`-reference_seqs_fp - Ref seqs to search against. [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] + Ref seqs to search against. [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] `-`-min_consensus_fraction Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query [default: 0.51] `-`-similarity diff --git a/doc/scripts/parallel_identify_chimeric_seqs.rst b/doc/scripts/parallel_identify_chimeric_seqs.rst index 096e3c3e6a..23cbe68e59 100644 --- a/doc/scripts/parallel_identify_chimeric_seqs.rst +++ b/doc/scripts/parallel_identify_chimeric_seqs.rst @@ -25,7 +25,7 @@ This script works like the `identify_chimeric_seqs.py <./identify_chimeric_seqs. **[OPTIONAL]** -a, `-`-aligned_reference_seqs_fp - Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.fasta] + Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/`85_otus.py <./85_otus.html>`_nast.fasta] -t, `-`-id_to_taxonomy_fp Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [default: None; REQUIRED when method is blast_fragments] -r, `-`-reference_seqs_fp diff --git a/doc/scripts/pick_closed_reference_otus.rst b/doc/scripts/pick_closed_reference_otus.rst index 55a611a0fc..d630d35cf7 100644 --- a/doc/scripts/pick_closed_reference_otus.rst +++ b/doc/scripts/pick_closed_reference_otus.rst @@ -42,11 +42,11 @@ Be aware that this doubles the amount of memory used. **[OPTIONAL]** -r, `-`-reference_fp - The reference sequences [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta]. NOTE: If you do not pass -r to this script, you will be using QIIME's default reference sequences. In this case, QIIME will copy the corresponding reference tree to the output directory. This is the tree that should be used to perform phylogenetic diversity analyses (e.g., with `core_diversity_analyses.py <./core_diversity_analyses.html>`_). + The reference sequences [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta]. NOTE: If you do not pass -r to this script, you will be using QIIME's default reference sequences. In this case, QIIME will copy the corresponding reference tree to the output directory. This is the tree that should be used to perform phylogenetic diversity analyses (e.g., with `core_diversity_analyses.py <./core_diversity_analyses.html>`_). -p, `-`-parameter_fp Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters . [if omitted, default values will be used] -t, `-`-taxonomy_fp - The taxonomy map [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] + The taxonomy map [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt] -s, `-`-assign_taxonomy Assign taxonomy to each sequence using `assign_taxonomy.py <./assign_taxonomy.html>`_ (this will override --taxonomy_fp, if provided) [default: False] -f, `-`-force diff --git a/doc/scripts/pick_open_reference_otus.rst b/doc/scripts/pick_open_reference_otus.rst index bf960563ec..46b0df8559 100644 --- a/doc/scripts/pick_open_reference_otus.rst +++ b/doc/scripts/pick_open_reference_otus.rst @@ -182,7 +182,7 @@ workflow. -m, `-`-otu_picking_method The OTU picking method to use for reference and de novo steps. Passing usearch61, for example, means that usearch61 will be used for the de novo steps and usearch61_ref will be used for reference steps. [default: uclust] -r, `-`-reference_fp - The reference sequences [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] + The reference sequences [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] -p, `-`-parameter_fp Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters . [if omitted, default values will be used] `-`-prefilter_refseqs_fp diff --git a/doc/scripts/pick_otus.rst b/doc/scripts/pick_otus.rst index 8880e33bff..8dd0ab52c4 100644 --- a/doc/scripts/pick_otus.rst +++ b/doc/scripts/pick_otus.rst @@ -81,7 +81,7 @@ The primary inputs for `pick_otus.py <./pick_otus.html>`_ are: -o, `-`-output_dir Path to store result file [default: ./_picked_otus/] -r, `-`-refseqs_fp - Path to reference sequences to search against when using -m blast, -m sortmerna, -m uclust_ref, -m usearch_ref, or -m usearch61_ref [default: /Users/jairideout/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] + Path to reference sequences to search against when using -m blast, -m sortmerna, -m uclust_ref, -m usearch_ref, or -m usearch61_ref [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta] -b, `-`-blast_db Pre-existing database to blast against when using -m blast [default: None] -e, `-`-max_e_value_blast @@ -101,7 +101,7 @@ The primary inputs for `pick_otus.py <./pick_otus.html>`_ are: `-`-min_aligned_percent Minimum percent of query sequence that can be aligned to consider a hit, expressed as a fraction between 0 and 1 (BLAST OTU picker only) [default: 0.5] -s, `-`-similarity - Sequence similarity threshold (for blast, cdhit, uclust, uclust_ref, usearch, usearch_ref, usearch61, usearch61_ref, sumaclust or sortmerna [default: 0.97] + Sequence similarity threshold (for blast, cdhit, uclust, uclust_ref, usearch, usearch_ref, usearch61, usearch61_ref, sumaclust, and sortmerna) [default: 0.97] `-`-sumaclust_exact A sequence is assigned to the best matching seed rather than the first matching seed passing the similarity threshold [default: False] `-`-sumaclust_l diff --git a/doc/scripts/split_libraries_fastq.rst b/doc/scripts/split_libraries_fastq.rst index 4f5d9b9c40..44c140bddb 100644 --- a/doc/scripts/split_libraries_fastq.rst +++ b/doc/scripts/split_libraries_fastq.rst @@ -33,7 +33,7 @@ `-`-store_qual_scores Store qual strings in .qual files [default: False] `-`-sample_ids - Comma-separated list of samples id to be applied to all sequences, must be one per input file path (used when data is not multiplexed) [default: None] + Comma-separated list of samples ids to be applied to all sequences, must be one per input file path (used when data is not multiplexed) [default: None] `-`-store_demultiplexed_fastq Write demultiplexed fastq files [default: False] `-`-retain_unassigned_reads @@ -57,7 +57,7 @@ `-`-last_bad_quality_char DEPRECATED: use -q instead. This method of setting is not robust to different versions of CASAVA. `-`-barcode_type - The type of barcode used. This can be an integer, e.g. for length 6 barcodes, or golay_12 for golay error-correcting barcodes. Error correction will only be applied for golay_12 barcodes. [default: golay_12] + The type of barcode used. This can be an integer, e.g. for length 6 barcodes, or "golay_12" for golay error-correcting barcodes. Error correction will only be applied for "golay_12" barcodes. If data is not barcoded, pass "not-barcoded". [default: golay_12] `-`-max_barcode_errors Maximum number of errors in barcode [default: 1.5] `-`-phred_offset @@ -91,12 +91,12 @@ :: - split_libraries_fastq.py -i lane1_read1.fastq.gz --sample_id my.sample.1 -o slout_single_sample_q20/ -q 19 --barcode_type 'not-barcoded' + split_libraries_fastq.py -i lane1_read1.fastq.gz --sample_ids my.sample.1 -o slout_single_sample_q20/ -q 19 --barcode_type 'not-barcoded' **Quality filter (at Phred >= Q20) two non-multiplexed lanes of Illumina fastq data with different samples in each and write results to ./slout_not_multiplexed_q20.:** :: - split_libraries_fastq.py -i lane1_read1.fastq.gz,lane2_read1.fastq.gz --sample_id my.sample.1,my.sample.2 -o slout_not_multiplexed_q20/ -q 19 --barcode_type 'not-barcoded' + split_libraries_fastq.py -i lane1_read1.fastq.gz,lane2_read1.fastq.gz --sample_ids my.sample.1,my.sample.2 -o slout_not_multiplexed_q20/ -q 19 --barcode_type 'not-barcoded' diff --git a/doc/scripts/start_parallel_jobs_slurm.rst b/doc/scripts/start_parallel_jobs_slurm.rst index 483f81bbf7..4a184d2e2a 100644 --- a/doc/scripts/start_parallel_jobs_slurm.rst +++ b/doc/scripts/start_parallel_jobs_slurm.rst @@ -29,6 +29,8 @@ This script is designed to start multiple jobs in parallel on cluster systems wi Megabytes of memory to request per CPU [default: slurm's default] -j, `-`-job_dir Directory to store the jobs [default: jobs/] + -t, `-`-time + Run time limit of the jobs in dd-hh:mm:ss format [default: slurm's default] **Output:** diff --git a/doc/scripts/summarize_taxa.rst b/doc/scripts/summarize_taxa.rst index 3c2c605ab6..10f6551297 100644 --- a/doc/scripts/summarize_taxa.rst +++ b/doc/scripts/summarize_taxa.rst @@ -7,7 +7,7 @@ **Description:** -The `summarize_taxa.py <./summarize_taxa.html>`_ script provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input. The taxonomic level for which the summary information is provided is designated with the -L option. The meaning of this level will depend on the format of the taxon strings that are returned from the taxonomy assignment step. The taxonomy strings that are most useful are those that standardize the taxonomic level with the depth in the taxonomic strings. For instance, for the RDP classifier taxonomy, Level 2 = Domain (e.g. Bacteria), 3 = Phylum (e.g. Firmicutes), 4 = Class (e.g. Clostridia), 5 = Order (e.g. Clostridiales), 6 = Family (e.g. Clostridiaceae), and 7 = Genus (e.g. Clostridium). By default, the relative abundance of each taxonomic group will be reported, but the raw counts can be returned if -a is passed. +The `summarize_taxa.py <./summarize_taxa.html>`_ script provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input. The taxonomic level for which the summary information is provided is designated with the -L option. The meaning of this level will depend on the format of the taxon strings that are returned from the taxonomy assignment step. The taxonomy strings that are most useful are those that standardize the taxonomic level with the depth in the taxonomic strings. For instance, the Greengenes database uses the following levels: Level 1 = Kingdom (e.g Bacteria), Level 2 = Phylum (e.g Actinobacteria), Level 3 = Class (e.g Actinobacteria), Level 4 = Order (e.g Actinomycetales), Level 5 = Family (e.g Streptomycetaceae), Level 6 = Genus (e.g Streptomyces), Level 7 = Species (e.g mirabilis). By default, the relative abundance of each taxonomic group will be reported, but the raw counts can be returned if -a is passed. By default, taxa summary tables will be output in both classic (tab-separated) and BIOM formats. The BIOM-formatted taxa summary tables can be used as input to other QIIME scripts that accept BIOM files. diff --git a/qiime/__init__.py b/qiime/__init__.py index 8341ee386f..7a09cdae81 100644 --- a/qiime/__init__.py +++ b/qiime/__init__.py @@ -18,7 +18,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/add_alpha_to_mapping_file.py b/qiime/add_alpha_to_mapping_file.py index 90c282a424..5940fa5f37 100755 --- a/qiime/add_alpha_to_mapping_file.py +++ b/qiime/add_alpha_to_mapping_file.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/qiime/add_qiime_labels.py b/qiime/add_qiime_labels.py index 25641190c2..a6bfba25f6 100755 --- a/qiime/add_qiime_labels.py +++ b/qiime/add_qiime_labels.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/adjust_seq_orientation.py b/qiime/adjust_seq_orientation.py index 5f0628abba..fcdb331d92 100755 --- a/qiime/adjust_seq_orientation.py +++ b/qiime/adjust_seq_orientation.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/align_seqs.py b/qiime/align_seqs.py index ea3522c8e1..3b382c318d 100644 --- a/qiime/align_seqs.py +++ b/qiime/align_seqs.py @@ -8,7 +8,7 @@ "Jeremy Widmann", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/alpha_diversity.py b/qiime/alpha_diversity.py index 01a9c5d250..b07faade22 100644 --- a/qiime/alpha_diversity.py +++ b/qiime/alpha_diversity.py @@ -6,7 +6,7 @@ "William Van Treuren", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/assign_taxonomy.py b/qiime/assign_taxonomy.py index 67f0521ced..fb619c81d3 100644 --- a/qiime/assign_taxonomy.py +++ b/qiime/assign_taxonomy.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Antonio Gonzalez Pena", "David Soergel", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/barcode.py b/qiime/barcode.py index 59cf615f07..237fe7cec8 100644 --- a/qiime/barcode.py +++ b/qiime/barcode.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/beta_diversity.py b/qiime/beta_diversity.py index 4371794ef2..9f878354a3 100644 --- a/qiime/beta_diversity.py +++ b/qiime/beta_diversity.py @@ -6,7 +6,7 @@ "Jose Carlos Clemente Litran", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/beta_metrics.py b/qiime/beta_metrics.py index a13158cfb9..09c52a3958 100644 --- a/qiime/beta_metrics.py +++ b/qiime/beta_metrics.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/biplots.py b/qiime/biplots.py index c82f7a14b8..7ca4d1224f 100644 --- a/qiime/biplots.py +++ b/qiime/biplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Justin Kuczynski"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/qiime/categorized_dist_scatterplot.py b/qiime/categorized_dist_scatterplot.py index c3855c3ad5..01e0b2e388 100755 --- a/qiime/categorized_dist_scatterplot.py +++ b/qiime/categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/check_id_map.py b/qiime/check_id_map.py index 4239cdae94..72278243f5 100644 --- a/qiime/check_id_map.py +++ b/qiime/check_id_map.py @@ -43,7 +43,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/qiime/clean_raxml_parsimony_tree.py b/qiime/clean_raxml_parsimony_tree.py index b37222f686..66b078356d 100644 --- a/qiime/clean_raxml_parsimony_tree.py +++ b/qiime/clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/cluster_quality.py b/qiime/cluster_quality.py index db02863680..a3e9a2c10d 100644 --- a/qiime/cluster_quality.py +++ b/qiime/cluster_quality.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" """ computes cluster quality the default way, bet/within""" diff --git a/qiime/collate_alpha.py b/qiime/collate_alpha.py index e73d0fb9d0..36d6758c3c 100644 --- a/qiime/collate_alpha.py +++ b/qiime/collate_alpha.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/colors.py b/qiime/colors.py index 3273c70c57..52729f3ebb 100644 --- a/qiime/colors.py +++ b/qiime/colors.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Rob Knight", "Jesse Stombaugh", "Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/compare_alpha_diversity.py b/qiime/compare_alpha_diversity.py index 6ea32ad023..e727bb33d0 100644 --- a/qiime/compare_alpha_diversity.py +++ b/qiime/compare_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/qiime/compare_categories.py b/qiime/compare_categories.py index 75c4c6f30d..9ecc88b844 100755 --- a/qiime/compare_categories.py +++ b/qiime/compare_categories.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_distance_matrices.py b/qiime/compare_distance_matrices.py index 62a594b5f8..007f850b33 100755 --- a/qiime/compare_distance_matrices.py +++ b/qiime/compare_distance_matrices.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_taxa_summaries.py b/qiime/compare_taxa_summaries.py index be6d0ea05f..cfa0bcb6ae 100755 --- a/qiime/compare_taxa_summaries.py +++ b/qiime/compare_taxa_summaries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_trajectories.py b/qiime/compare_trajectories.py index 492290413d..6e02935496 100644 --- a/qiime/compare_trajectories.py +++ b/qiime/compare_trajectories.py @@ -5,7 +5,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/qiime/compute_taxonomy_ratios.py b/qiime/compute_taxonomy_ratios.py index 897377e85e..f9febcc6e4 100644 --- a/qiime/compute_taxonomy_ratios.py +++ b/qiime/compute_taxonomy_ratios.py @@ -11,7 +11,7 @@ __copyright__ = "Copyright 2014, The QIIME project" __credits__ = ["Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/qiime/convert_fastaqual_fastq.py b/qiime/convert_fastaqual_fastq.py index 017bf2970f..fcd150d840 100644 --- a/qiime/convert_fastaqual_fastq.py +++ b/qiime/convert_fastaqual_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/qiime/core_microbiome.py b/qiime/core_microbiome.py index ab19d3fe54..c816219a36 100644 --- a/qiime/core_microbiome.py +++ b/qiime/core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/demultiplex_fasta.py b/qiime/demultiplex_fasta.py index f3eefb7f2c..1c1b15b6f5 100755 --- a/qiime/demultiplex_fasta.py +++ b/qiime/demultiplex_fasta.py @@ -13,7 +13,7 @@ "Jens Reeder", "Emily TerAvest"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/qiime/denoise_wrapper.py b/qiime/denoise_wrapper.py index 2e9964589d..04b9d3fd53 100644 --- a/qiime/denoise_wrapper.py +++ b/qiime/denoise_wrapper.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/denoiser/__init__.py b/qiime/denoiser/__init__.py index 8d4805cb8c..c8d59336c4 100644 --- a/qiime/denoiser/__init__.py +++ b/qiime/denoiser/__init__.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/cluster_utils.py b/qiime/denoiser/cluster_utils.py index ef617c60ff..5159938690 100644 --- a/qiime/denoiser/cluster_utils.py +++ b/qiime/denoiser/cluster_utils.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/denoise_postprocess.py b/qiime/denoiser/denoise_postprocess.py index 8acec22e39..27c653acf0 100644 --- a/qiime/denoiser/denoise_postprocess.py +++ b/qiime/denoiser/denoise_postprocess.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/denoise_worker.py b/qiime/denoiser/denoise_worker.py index 30f84ce948..ab751da856 100644 --- a/qiime/denoiser/denoise_worker.py +++ b/qiime/denoiser/denoise_worker.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/flowgram_clustering.py b/qiime/denoiser/flowgram_clustering.py index c33119615f..9e8dec5421 100644 --- a/qiime/denoiser/flowgram_clustering.py +++ b/qiime/denoiser/flowgram_clustering.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/flowgram_filter.py b/qiime/denoiser/flowgram_filter.py index 0cde5567d1..6be4112358 100644 --- a/qiime/denoiser/flowgram_filter.py +++ b/qiime/denoiser/flowgram_filter.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/make_cluster_jobs.py b/qiime/denoiser/make_cluster_jobs.py index eddbad8f56..ed4cbaa2ff 100755 --- a/qiime/denoiser/make_cluster_jobs.py +++ b/qiime/denoiser/make_cluster_jobs.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/preprocess.py b/qiime/denoiser/preprocess.py index c885f1a116..8ebe79c9c5 100644 --- a/qiime/denoiser/preprocess.py +++ b/qiime/denoiser/preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/utils.py b/qiime/denoiser/utils.py index 8d1a50247f..a87bd9aa75 100644 --- a/qiime/denoiser/utils.py +++ b/qiime/denoiser/utils.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/detrend.py b/qiime/detrend.py index f5785ccc3e..6e8c4aa22e 100644 --- a/qiime/detrend.py +++ b/qiime/detrend.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2012, The QIIME Project" __credits__ = ["Dan Knights", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/qiime/differential_abundance.py b/qiime/differential_abundance.py index f42599e27c..0f6859513a 100755 --- a/qiime/differential_abundance.py +++ b/qiime/differential_abundance.py @@ -17,7 +17,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss", "Joseph Paulson"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/qiime/distance_matrix_from_mapping.py b/qiime/distance_matrix_from_mapping.py index 9b6aacfa44..ab4fd04c93 100644 --- a/qiime/distance_matrix_from_mapping.py +++ b/qiime/distance_matrix_from_mapping.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Andrew J. King"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/qiime/estimate_observation_richness.py b/qiime/estimate_observation_richness.py index 1b06d1dbfa..37cbe845d9 100755 --- a/qiime/estimate_observation_richness.py +++ b/qiime/estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/exclude_seqs_by_blast.py b/qiime/exclude_seqs_by_blast.py index 447209a36d..9bd8ee5a27 100644 --- a/qiime/exclude_seqs_by_blast.py +++ b/qiime/exclude_seqs_by_blast.py @@ -17,7 +17,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Zaneveld", "Rob Knight", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/qiime/extract_barcodes.py b/qiime/extract_barcodes.py index 19010a21c1..1dba62f0f4 100644 --- a/qiime/extract_barcodes.py +++ b/qiime/extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/qiime/filter.py b/qiime/filter.py index 5959e59f3d..875bc9152f 100644 --- a/qiime/filter.py +++ b/qiime/filter.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Will Van Treuren", "Daniel McDonald", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/filter_alignment.py b/qiime/filter_alignment.py index 075f09ea2d..9cb4f88614 100755 --- a/qiime/filter_alignment.py +++ b/qiime/filter_alignment.py @@ -21,7 +21,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/filter_otus_by_sample.py b/qiime/filter_otus_by_sample.py index 2df2fbeb8f..e173cd34dc 100644 --- a/qiime/filter_otus_by_sample.py +++ b/qiime/filter_otus_by_sample.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/format.py b/qiime/format.py index d326e7257f..4541003d64 100755 --- a/qiime/format.py +++ b/qiime/format.py @@ -6,7 +6,7 @@ "Antonio Gonzalez Pena", "Daniel McDonald", "Jai Ram Rideout"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/golay.py b/qiime/golay.py index 16509cff73..7e4a81a91d 100644 --- a/qiime/golay.py +++ b/qiime/golay.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/group.py b/qiime/group.py index cc8b559720..667df79db4 100755 --- a/qiime/group.py +++ b/qiime/group.py @@ -8,7 +8,7 @@ "Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/hamming.py b/qiime/hamming.py index 2da566f26d..7ab25ff497 100644 --- a/qiime/hamming.py +++ b/qiime/hamming.py @@ -15,7 +15,7 @@ # remember to add yourself if you make changes __credits__ = ["Micah Hamady", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/hierarchical_cluster.py b/qiime/hierarchical_cluster.py index da576823a0..338a1ca10e 100644 --- a/qiime/hierarchical_cluster.py +++ b/qiime/hierarchical_cluster.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/identify_chimeric_seqs.py b/qiime/identify_chimeric_seqs.py index c5681e6f73..921ac07fef 100755 --- a/qiime/identify_chimeric_seqs.py +++ b/qiime/identify_chimeric_seqs.py @@ -28,7 +28,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "William Walters", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/join_paired_ends.py b/qiime/join_paired_ends.py index c94ebe5e7b..a599daf99f 100644 --- a/qiime/join_paired_ends.py +++ b/qiime/join_paired_ends.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/qiime/make_2d_plots.py b/qiime/make_2d_plots.py index 3f81e94631..f185d47141 100644 --- a/qiime/make_2d_plots.py +++ b/qiime/make_2d_plots.py @@ -7,7 +7,7 @@ # remember to add yourself __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/make_bipartite_network.py b/qiime/make_bipartite_network.py index f03a3f9064..f6869a211d 100644 --- a/qiime/make_bipartite_network.py +++ b/qiime/make_bipartite_network.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Will Van Treuren, Julia Goodrich"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/qiime/make_bootstrapped_tree.py b/qiime/make_bootstrapped_tree.py index 570f484a09..424a5e7520 100644 --- a/qiime/make_bootstrapped_tree.py +++ b/qiime/make_bootstrapped_tree.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/make_distance_boxplots.py b/qiime/make_distance_boxplots.py index 088c8d738b..6dccc2c0f9 100755 --- a/qiime/make_distance_boxplots.py +++ b/qiime/make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/make_fastq.py b/qiime/make_fastq.py index 6aa6e20a88..d7d0b7f6d8 100644 --- a/qiime/make_fastq.py +++ b/qiime/make_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_library_id_lists.py b/qiime/make_library_id_lists.py index da309fecdb..8ea5be4558 100644 --- a/qiime/make_library_id_lists.py +++ b/qiime/make_library_id_lists.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_otu_heatmap.py b/qiime/make_otu_heatmap.py index cd07d9a71a..6caaee4975 100644 --- a/qiime/make_otu_heatmap.py +++ b/qiime/make_otu_heatmap.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Dan Knights", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/qiime/make_otu_network.py b/qiime/make_otu_network.py index 37ba9c9d86..ece2051a10 100644 --- a/qiime/make_otu_network.py +++ b/qiime/make_otu_network.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Julia Goodrich"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/qiime/make_otu_table.py b/qiime/make_otu_table.py index 7b47cbcc02..303418b1c1 100644 --- a/qiime/make_otu_table.py +++ b/qiime/make_otu_table.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Justin Kuczynski", "Adam Robbins-Pianka", "Sami Pietila"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/make_per_library_sff.py b/qiime/make_per_library_sff.py index 494bad3378..ab0cb2bc13 100644 --- a/qiime/make_per_library_sff.py +++ b/qiime/make_per_library_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_phylogeny.py b/qiime/make_phylogeny.py index 83d49ca9ac..d549e4e921 100644 --- a/qiime/make_phylogeny.py +++ b/qiime/make_phylogeny.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Justin Kuczynski", "Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/make_rarefaction_plots.py b/qiime/make_rarefaction_plots.py index 3182147779..7074641e35 100644 --- a/qiime/make_rarefaction_plots.py +++ b/qiime/make_rarefaction_plots.py @@ -7,7 +7,7 @@ "Will Van Treuren", "Yoshiki Vazquez Baeza", "Jai Ram Rideout", "Evan Bolyen"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/map_reads_to_reference.py b/qiime/map_reads_to_reference.py index 207756f404..83c8ea54aa 100644 --- a/qiime/map_reads_to_reference.py +++ b/qiime/map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/nmds.py b/qiime/nmds.py index 789ac81fbf..dbc43402dc 100644 --- a/qiime/nmds.py +++ b/qiime/nmds.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/normalize_table.py b/qiime/normalize_table.py index da333f423a..46fd67e8d5 100755 --- a/qiime/normalize_table.py +++ b/qiime/normalize_table.py @@ -15,7 +15,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss", "Joseph Paulson"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/qiime/otu_significance.py b/qiime/otu_significance.py index 7480d3566f..a43049cff9 100644 --- a/qiime/otu_significance.py +++ b/qiime/otu_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren", "Luke Ursell", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Luke Ursell" __email__ = "lkursell@gmail.com" diff --git a/qiime/parallel/__init__.py b/qiime/parallel/__init__.py index a7e9d0cf37..b27bf6a049 100644 --- a/qiime/parallel/__init__.py +++ b/qiime/parallel/__init__.py @@ -20,7 +20,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/align_seqs.py b/qiime/parallel/align_seqs.py index 22d0b47eff..87055a72b4 100644 --- a/qiime/parallel/align_seqs.py +++ b/qiime/parallel/align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/alpha_diversity.py b/qiime/parallel/alpha_diversity.py index de19d33bda..630c825785 100644 --- a/qiime/parallel/alpha_diversity.py +++ b/qiime/parallel/alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/assign_taxonomy.py b/qiime/parallel/assign_taxonomy.py index 088b0d4b92..6a2dd9aecc 100644 --- a/qiime/parallel/assign_taxonomy.py +++ b/qiime/parallel/assign_taxonomy.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/beta_diversity.py b/qiime/parallel/beta_diversity.py index 9d70e0b3e5..7d98054b56 100644 --- a/qiime/parallel/beta_diversity.py +++ b/qiime/parallel/beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/blast.py b/qiime/parallel/blast.py index d58efbd1fc..fe6c5a9f1a 100755 --- a/qiime/parallel/blast.py +++ b/qiime/parallel/blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/identify_chimeric_seqs.py b/qiime/parallel/identify_chimeric_seqs.py index 38b0ea46dc..5be410b5cf 100755 --- a/qiime/parallel/identify_chimeric_seqs.py +++ b/qiime/parallel/identify_chimeric_seqs.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/map_reads_to_reference.py b/qiime/parallel/map_reads_to_reference.py index ae8bd898b7..9fd3c93169 100644 --- a/qiime/parallel/map_reads_to_reference.py +++ b/qiime/parallel/map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/merge_otus.py b/qiime/parallel/merge_otus.py index 64fdf4a5df..530800f9d3 100644 --- a/qiime/parallel/merge_otus.py +++ b/qiime/parallel/merge_otus.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/qiime/parallel/multiple_rarefactions.py b/qiime/parallel/multiple_rarefactions.py index dea20da286..4a9b824648 100644 --- a/qiime/parallel/multiple_rarefactions.py +++ b/qiime/parallel/multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/pick_otus.py b/qiime/parallel/pick_otus.py index 7cee5ee823..b4cabd2046 100644 --- a/qiime/parallel/pick_otus.py +++ b/qiime/parallel/pick_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/poller.py b/qiime/parallel/poller.py index dcef765059..3880c8c7d6 100755 --- a/qiime/parallel/poller.py +++ b/qiime/parallel/poller.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/util.py b/qiime/parallel/util.py index c1fd625de2..0c83d1eb44 100644 --- a/qiime/parallel/util.py +++ b/qiime/parallel/util.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parse.py b/qiime/parse.py index 62d7729927..e3070d6217 100644 --- a/qiime/parse.py +++ b/qiime/parse.py @@ -8,7 +8,7 @@ "Antonio Gonzalez Pena", "Jai Ram Rideout", "Will Van Treuren", "Yoshiki Vazquez-Baeza", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/pick_otus.py b/qiime/pick_otus.py index ac6b3ffc65..20d697755b 100644 --- a/qiime/pick_otus.py +++ b/qiime/pick_otus.py @@ -5,7 +5,7 @@ "William Walters", "Jose Carlos Clemente Litran", "Adam Robbins-Pianka", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/pick_rep_set.py b/qiime/pick_rep_set.py index 7220afd05f..efcb16f874 100644 --- a/qiime/pick_rep_set.py +++ b/qiime/pick_rep_set.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/qiime/plot_rank_abundance_graph.py b/qiime/plot_rank_abundance_graph.py index c46ffa3691..4427a48cd5 100644 --- a/qiime/plot_rank_abundance_graph.py +++ b/qiime/plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/plot_semivariogram.py b/qiime/plot_semivariogram.py index d598d82cb2..aebc3a696f 100644 --- a/qiime/plot_semivariogram.py +++ b/qiime/plot_semivariogram.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/qiime/plot_taxa_summary.py b/qiime/plot_taxa_summary.py index 49590c7cfd..94ba40dedb 100644 --- a/qiime/plot_taxa_summary.py +++ b/qiime/plot_taxa_summary.py @@ -7,7 +7,7 @@ __credits__ = ["Jesse Stobmaugh", "Julia Goodrich", "Micah Hamady"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/principal_coordinates.py b/qiime/principal_coordinates.py index 25188d5f79..d96f79877f 100644 --- a/qiime/principal_coordinates.py +++ b/qiime/principal_coordinates.py @@ -8,7 +8,7 @@ "Catherine Lozupone", "Emily TerAvest", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/process_sff.py b/qiime/process_sff.py index 6d0239b8e4..836f10da38 100644 --- a/qiime/process_sff.py +++ b/qiime/process_sff.py @@ -29,7 +29,7 @@ "Adam Robbins-Pianka", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/pycogent_backports/__init__.py b/qiime/pycogent_backports/__init__.py index a47bdac19e..f4066ad44c 100644 --- a/qiime/pycogent_backports/__init__.py +++ b/qiime/pycogent_backports/__init__.py @@ -18,6 +18,6 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/quality_scores_plot.py b/qiime/quality_scores_plot.py index 97a78ea39c..e84d694489 100755 --- a/qiime/quality_scores_plot.py +++ b/qiime/quality_scores_plot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/rarefaction.py b/qiime/rarefaction.py index eaa107862d..066aaf36b0 100644 --- a/qiime/rarefaction.py +++ b/qiime/rarefaction.py @@ -6,7 +6,7 @@ __credits__ = ["Justin Kuczynski", "Jose Carlos Clemente Litran", "Rob Knight", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/relatedness_library.py b/qiime/relatedness_library.py index c0bb395219..420d4bb259 100644 --- a/qiime/relatedness_library.py +++ b/qiime/relatedness_library.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/qiime/remote.py b/qiime/remote.py index fe35e1de97..9d33dd70c2 100755 --- a/qiime/remote.py +++ b/qiime/remote.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/shared_phylotypes.py b/qiime/shared_phylotypes.py index 06333bb60c..f57a0dd15e 100644 --- a/qiime/shared_phylotypes.py +++ b/qiime/shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder, Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/qiime/simsam.py b/qiime/simsam.py index fe26362495..6764066ed2 100755 --- a/qiime/simsam.py +++ b/qiime/simsam.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/sort.py b/qiime/sort.py index beee7c9185..11a591a8bc 100644 --- a/qiime/sort.py +++ b/qiime/sort.py @@ -13,7 +13,7 @@ __credits__ = ["Greg Caporaso", "Rob Knight", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split.py b/qiime/split.py index 74d8b05930..cf3a48946a 100644 --- a/qiime/split.py +++ b/qiime/split.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Daniel McDonald", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split_libraries.py b/qiime/split_libraries.py index 7a6e699c7f..bfc07a6a92 100644 --- a/qiime/split_libraries.py +++ b/qiime/split_libraries.py @@ -30,7 +30,7 @@ "Jesse Stombaugh", "William Walters", "Jens Reeder", "Emily TerAvest", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "rob@spot.colorado.edu, william.a.walters@colorado.edu" diff --git a/qiime/split_libraries_fastq.py b/qiime/split_libraries_fastq.py index e1e270b55d..4663977918 100644 --- a/qiime/split_libraries_fastq.py +++ b/qiime/split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split_libraries_lea_seq.py b/qiime/split_libraries_lea_seq.py index 929e919432..c55c866f4a 100644 --- a/qiime/split_libraries_lea_seq.py +++ b/qiime/split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/qiime/stats.py b/qiime/stats.py index 9d6f89cf20..9fe59e4ee3 100644 --- a/qiime/stats.py +++ b/qiime/stats.py @@ -8,7 +8,7 @@ "Jose Carlos Clemente Litran", "Greg Caporaso", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/summarize_taxa.py b/qiime/summarize_taxa.py index c3e329e91f..3a6c830c0a 100644 --- a/qiime/summarize_taxa.py +++ b/qiime/summarize_taxa.py @@ -6,7 +6,7 @@ "Rob Knight", "Catherine Lozupone", "Justin Kuczynski", "Julia Goodrich", "Antonio Gonzalez Pena", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/qiime/supervised_learning.py b/qiime/supervised_learning.py index 8a3ff5669d..ce20c17572 100644 --- a/qiime/supervised_learning.py +++ b/qiime/supervised_learning.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Luke Ursell", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/qiime/support_files/R/util.r b/qiime/support_files/R/util.r index 55694975e3..c2d7c8e27f 100644 --- a/qiime/support_files/R/util.r +++ b/qiime/support_files/R/util.r @@ -4,7 +4,7 @@ # __copyright__ = "Copyright 2011, The QIIME Project" # __credits__ = ["Dan Knights"] # __license__ = "GPL" -# __version__ = "1.9.0-dev" +# __version__ = "1.9.1" # __maintainer__ = "Dan Knights" # __email__ = "daniel.knights@colorado.edu" # diff --git a/qiime/support_files/js/otu_count_display.js b/qiime/support_files/js/otu_count_display.js index e38195f51d..293913e014 100644 --- a/qiime/support_files/js/otu_count_display.js +++ b/qiime/support_files/js/otu_count_display.js @@ -6,7 +6,7 @@ __author__ = "Jesse Stombaugh" __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] #remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Rob Knight" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/support_files/test_js/test_otu_count_display.html b/qiime/support_files/test_js/test_otu_count_display.html index 859c37ca8b..b2d3796d3f 100644 --- a/qiime/support_files/test_js/test_otu_count_display.html +++ b/qiime/support_files/test_js/test_otu_count_display.html @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" #consider project name __credits__ = ["Jesse Stombaugh"] #remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/test.py b/qiime/test.py index 0a8fa0cc9e..5a745d020b 100644 --- a/qiime/test.py +++ b/qiime/test.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/transform_coordinate_matrices.py b/qiime/transform_coordinate_matrices.py index 6bd8f42a45..ee323a8636 100644 --- a/qiime/transform_coordinate_matrices.py +++ b/qiime/transform_coordinate_matrices.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Kyle Patnode", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/tree_compare.py b/qiime/tree_compare.py index 4c85ec6eaf..1fae931c96 100644 --- a/qiime/tree_compare.py +++ b/qiime/tree_compare.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/trim_sff_primers.py b/qiime/trim_sff_primers.py index f07968284a..8c37dc5753 100644 --- a/qiime/trim_sff_primers.py +++ b/qiime/trim_sff_primers.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", 'Kyle Bittinger', "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/truncate_fasta_qual_files.py b/qiime/truncate_fasta_qual_files.py index 55b97cdfe2..c8177582e9 100755 --- a/qiime/truncate_fasta_qual_files.py +++ b/qiime/truncate_fasta_qual_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/truncate_reverse_primer.py b/qiime/truncate_reverse_primer.py index fb6cbf5358..f112a6ed71 100755 --- a/qiime/truncate_reverse_primer.py +++ b/qiime/truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/util.py b/qiime/util.py index f86f520317..9d91d79c04 100644 --- a/qiime/util.py +++ b/qiime/util.py @@ -8,7 +8,7 @@ "Levi McCracken", "Damien Coy", "Yoshiki Vazquez Baeza", "Will Van Treuren", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/validate_demultiplexed_fasta.py b/qiime/validate_demultiplexed_fasta.py index dcaf728bd7..6f8d7c0281 100755 --- a/qiime/validate_demultiplexed_fasta.py +++ b/qiime/validate_demultiplexed_fasta.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/qiime/workflow/__init__.py b/qiime/workflow/__init__.py index 9a7443f804..5395b15e8a 100644 --- a/qiime/workflow/__init__.py +++ b/qiime/workflow/__init__.py @@ -21,6 +21,6 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/ampliconnoise.py b/qiime/workflow/ampliconnoise.py index 41e6b2b83d..b318c23d0f 100755 --- a/qiime/workflow/ampliconnoise.py +++ b/qiime/workflow/ampliconnoise.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/core_diversity_analyses.py b/qiime/workflow/core_diversity_analyses.py index 7bec94125b..a95f953412 100644 --- a/qiime/workflow/core_diversity_analyses.py +++ b/qiime/workflow/core_diversity_analyses.py @@ -23,7 +23,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/downstream.py b/qiime/workflow/downstream.py index 0068e0b5d7..3785638349 100644 --- a/qiime/workflow/downstream.py +++ b/qiime/workflow/downstream.py @@ -8,7 +8,7 @@ "Jesse Stombaugh", "Yoshiki Vazquez Baeza", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/pick_open_reference_otus.py b/qiime/workflow/pick_open_reference_otus.py index a28532bea2..71a1b7c56e 100644 --- a/qiime/workflow/pick_open_reference_otus.py +++ b/qiime/workflow/pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/preprocess.py b/qiime/workflow/preprocess.py index 887afdf7c8..bddb431798 100644 --- a/qiime/workflow/preprocess.py +++ b/qiime/workflow/preprocess.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/workflow/upstream.py b/qiime/workflow/upstream.py index 4fb73a131d..fd146c2903 100644 --- a/qiime/workflow/upstream.py +++ b/qiime/workflow/upstream.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/util.py b/qiime/workflow/util.py index ccb2065821..39224ee28b 100755 --- a/qiime/workflow/util.py +++ b/qiime/workflow/util.py @@ -8,7 +8,7 @@ "Kyle Bittinger", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/add_alpha_to_mapping_file.py b/scripts/add_alpha_to_mapping_file.py index 03ff38fa1c..7e561fff7d 100755 --- a/scripts/add_alpha_to_mapping_file.py +++ b/scripts/add_alpha_to_mapping_file.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/scripts/add_qiime_labels.py b/scripts/add_qiime_labels.py index 1a669ed1b8..cf7669d5b9 100755 --- a/scripts/add_qiime_labels.py +++ b/scripts/add_qiime_labels.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/adjust_seq_orientation.py b/scripts/adjust_seq_orientation.py index 6c89d6c98d..f24363669b 100755 --- a/scripts/adjust_seq_orientation.py +++ b/scripts/adjust_seq_orientation.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/align_seqs.py b/scripts/align_seqs.py index 62c9e4988b..563affe7af 100755 --- a/scripts/align_seqs.py +++ b/scripts/align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/alpha_diversity.py b/scripts/alpha_diversity.py index 64ff78b275..ff76991667 100755 --- a/scripts/alpha_diversity.py +++ b/scripts/alpha_diversity.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/alpha_rarefaction.py b/scripts/alpha_rarefaction.py index 12cddf6039..74101b18f8 100755 --- a/scripts/alpha_rarefaction.py +++ b/scripts/alpha_rarefaction.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/ampliconnoise.py b/scripts/ampliconnoise.py index fc3af6212f..186e09e2fe 100755 --- a/scripts/ampliconnoise.py +++ b/scripts/ampliconnoise.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jose A. Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/assign_taxonomy.py b/scripts/assign_taxonomy.py index deeedebf2a..8578df782e 100755 --- a/scripts/assign_taxonomy.py +++ b/scripts/assign_taxonomy.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Antonio Gonzalez Pena", "David Soergel", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/beta_diversity.py b/scripts/beta_diversity.py index 80f0bc0f15..8792fdf2be 100755 --- a/scripts/beta_diversity.py +++ b/scripts/beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/beta_diversity_through_plots.py b/scripts/beta_diversity_through_plots.py index 0b280b27b4..da38f32ab7 100755 --- a/scripts/beta_diversity_through_plots.py +++ b/scripts/beta_diversity_through_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kestrel Gorlick"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/beta_significance.py b/scripts/beta_significance.py index 1fe27261bc..62a91d699d 100755 --- a/scripts/beta_significance.py +++ b/scripts/beta_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jose Antonio Navas", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/blast_wrapper.py b/scripts/blast_wrapper.py index 45f3a681f5..5f38aea179 100755 --- a/scripts/blast_wrapper.py +++ b/scripts/blast_wrapper.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/categorized_dist_scatterplot.py b/scripts/categorized_dist_scatterplot.py index a07e5da549..3ee6aa3b25 100755 --- a/scripts/categorized_dist_scatterplot.py +++ b/scripts/categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/check_id_map.py b/scripts/check_id_map.py index c4bd37dc34..2d6b2e2e0f 100755 --- a/scripts/check_id_map.py +++ b/scripts/check_id_map.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/clean_raxml_parsimony_tree.py b/scripts/clean_raxml_parsimony_tree.py index dde13f4281..0bff203ad1 100755 --- a/scripts/clean_raxml_parsimony_tree.py +++ b/scripts/clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/cluster_quality.py b/scripts/cluster_quality.py index 5080b9bfe2..8a2383775a 100755 --- a/scripts/cluster_quality.py +++ b/scripts/cluster_quality.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/collapse_samples.py b/scripts/collapse_samples.py index 28185fb151..c063291f10 100755 --- a/scripts/collapse_samples.py +++ b/scripts/collapse_samples.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/collate_alpha.py b/scripts/collate_alpha.py index 84c4c408ca..be94a40d4b 100755 --- a/scripts/collate_alpha.py +++ b/scripts/collate_alpha.py @@ -15,7 +15,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/compare_alpha_diversity.py b/scripts/compare_alpha_diversity.py index 707ed01379..b2d9beb733 100755 --- a/scripts/compare_alpha_diversity.py +++ b/scripts/compare_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caparaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/scripts/compare_categories.py b/scripts/compare_categories.py index de994054ec..672b6c7919 100755 --- a/scripts/compare_categories.py +++ b/scripts/compare_categories.py @@ -6,7 +6,7 @@ __credits__ = ["Logan Knecht", "Michael Dwan", "Damien Coy", "Jai Ram Rideout", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_distance_matrices.py b/scripts/compare_distance_matrices.py index 42ed777d8b..96c1147106 100755 --- a/scripts/compare_distance_matrices.py +++ b/scripts/compare_distance_matrices.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_taxa_summaries.py b/scripts/compare_taxa_summaries.py index 249b63a533..ba7b850385 100755 --- a/scripts/compare_taxa_summaries.py +++ b/scripts/compare_taxa_summaries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_trajectories.py b/scripts/compare_trajectories.py index 6e9fbbdd3c..030f2d1f10 100755 --- a/scripts/compare_trajectories.py +++ b/scripts/compare_trajectories.py @@ -6,7 +6,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/scripts/compute_core_microbiome.py b/scripts/compute_core_microbiome.py index ea0cdce7c0..909b6c8bea 100755 --- a/scripts/compute_core_microbiome.py +++ b/scripts/compute_core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/compute_taxonomy_ratios.py b/scripts/compute_taxonomy_ratios.py index d71d5e9549..c383b15630 100755 --- a/scripts/compute_taxonomy_ratios.py +++ b/scripts/compute_taxonomy_ratios.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/conditional_uncovered_probability.py b/scripts/conditional_uncovered_probability.py index e396b93c9a..977876814c 100755 --- a/scripts/conditional_uncovered_probability.py +++ b/scripts/conditional_uncovered_probability.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/consensus_tree.py b/scripts/consensus_tree.py index 64dadf56cf..66d80403ca 100755 --- a/scripts/consensus_tree.py +++ b/scripts/consensus_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "justinak@gmail.com" diff --git a/scripts/convert_fastaqual_fastq.py b/scripts/convert_fastaqual_fastq.py index 1001777161..a144a58a72 100755 --- a/scripts/convert_fastaqual_fastq.py +++ b/scripts/convert_fastaqual_fastq.py @@ -5,7 +5,7 @@ __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/scripts/convert_unifrac_sample_mapping_to_otu_table.py b/scripts/convert_unifrac_sample_mapping_to_otu_table.py index 55217c600a..9dfac289d1 100755 --- a/scripts/convert_unifrac_sample_mapping_to_otu_table.py +++ b/scripts/convert_unifrac_sample_mapping_to_otu_table.py @@ -5,7 +5,7 @@ __credits__ = ["Catherine Lozupone", "Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Cathy Lozupone" __email__ = "lozupone@colorado.edu" diff --git a/scripts/core_diversity_analyses.py b/scripts/core_diversity_analyses.py index 88a7d42526..5ef866365e 100755 --- a/scripts/core_diversity_analyses.py +++ b/scripts/core_diversity_analyses.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/count_seqs.py b/scripts/count_seqs.py index 4a53ca9a63..d33e30d955 100755 --- a/scripts/count_seqs.py +++ b/scripts/count_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/demultiplex_fasta.py b/scripts/demultiplex_fasta.py index c6f3e6e760..d334a39aac 100755 --- a/scripts/demultiplex_fasta.py +++ b/scripts/demultiplex_fasta.py @@ -13,7 +13,7 @@ "Jens Reeder", "Jose Antonio Navas Molina"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/scripts/denoise_wrapper.py b/scripts/denoise_wrapper.py index 399c678580..903c09fc64 100755 --- a/scripts/denoise_wrapper.py +++ b/scripts/denoise_wrapper.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser.py b/scripts/denoiser.py index 6e95c5bc70..14980550e7 100755 --- a/scripts/denoiser.py +++ b/scripts/denoiser.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser_preprocess.py b/scripts/denoiser_preprocess.py index 6e62fd7c53..15ef595bc1 100755 --- a/scripts/denoiser_preprocess.py +++ b/scripts/denoiser_preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser_worker.py b/scripts/denoiser_worker.py index e9782c2314..3373864f9a 100755 --- a/scripts/denoiser_worker.py +++ b/scripts/denoiser_worker.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/detrend.py b/scripts/detrend.py index 0921ae865d..62da2653f1 100755 --- a/scripts/detrend.py +++ b/scripts/detrend.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME Project" __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/scripts/differential_abundance.py b/scripts/differential_abundance.py index 5ec2e25712..018bd8f1ee 100755 --- a/scripts/differential_abundance.py +++ b/scripts/differential_abundance.py @@ -12,7 +12,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/scripts/dissimilarity_mtx_stats.py b/scripts/dissimilarity_mtx_stats.py index dfcdcbda18..4c066374d8 100755 --- a/scripts/dissimilarity_mtx_stats.py +++ b/scripts/dissimilarity_mtx_stats.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/distance_matrix_from_mapping.py b/scripts/distance_matrix_from_mapping.py index eee537b8e7..6bd2e1ef37 100755 --- a/scripts/distance_matrix_from_mapping.py +++ b/scripts/distance_matrix_from_mapping.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Andrew J. King"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/estimate_observation_richness.py b/scripts/estimate_observation_richness.py index 4e57957978..6be690022e 100755 --- a/scripts/estimate_observation_richness.py +++ b/scripts/estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/exclude_seqs_by_blast.py b/scripts/exclude_seqs_by_blast.py index 93c4cadf4a..6f24649517 100755 --- a/scripts/exclude_seqs_by_blast.py +++ b/scripts/exclude_seqs_by_blast.py @@ -26,7 +26,7 @@ "Jose Antonio Navas Molina", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/scripts/extract_barcodes.py b/scripts/extract_barcodes.py index ce774f92f0..49259331c9 100755 --- a/scripts/extract_barcodes.py +++ b/scripts/extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/extract_reads_from_interleaved_file.py b/scripts/extract_reads_from_interleaved_file.py index 1f61205663..d231be66ce 100755 --- a/scripts/extract_reads_from_interleaved_file.py +++ b/scripts/extract_reads_from_interleaved_file.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/extract_seqs_by_sample_id.py b/scripts/extract_seqs_by_sample_id.py index 9017b5e8a2..9896df0d76 100755 --- a/scripts/extract_seqs_by_sample_id.py +++ b/scripts/extract_seqs_by_sample_id.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_alignment.py b/scripts/filter_alignment.py index c5ac04176c..4f97a7dd87 100755 --- a/scripts/filter_alignment.py +++ b/scripts/filter_alignment.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Dan Knights", "Doug Wendel", "William Walters", "John Chase"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_distance_matrix.py b/scripts/filter_distance_matrix.py index 0619a8e7e0..00a721cf71 100755 --- a/scripts/filter_distance_matrix.py +++ b/scripts/filter_distance_matrix.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2010, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_fasta.py b/scripts/filter_fasta.py index e8114fe2aa..9277da0416 100755 --- a/scripts/filter_fasta.py +++ b/scripts/filter_fasta.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jens Reeder", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_otus_by_sample.py b/scripts/filter_otus_by_sample.py index 2816f67226..877dfaf56b 100755 --- a/scripts/filter_otus_by_sample.py +++ b/scripts/filter_otus_by_sample.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/filter_otus_from_otu_table.py b/scripts/filter_otus_from_otu_table.py index b549d5d59b..6c7c73a52a 100755 --- a/scripts/filter_otus_from_otu_table.py +++ b/scripts/filter_otus_from_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_samples_from_otu_table.py b/scripts/filter_samples_from_otu_table.py index bd5889d668..04e6105526 100755 --- a/scripts/filter_samples_from_otu_table.py +++ b/scripts/filter_samples_from_otu_table.py @@ -11,7 +11,7 @@ "Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_taxa_from_otu_table.py b/scripts/filter_taxa_from_otu_table.py index 0976f8b0f3..7765a3fa73 100755 --- a/scripts/filter_taxa_from_otu_table.py +++ b/scripts/filter_taxa_from_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_tree.py b/scripts/filter_tree.py index 52d13ae68b..21aaef1b4c 100755 --- a/scripts/filter_tree.py +++ b/scripts/filter_tree.py @@ -10,7 +10,7 @@ "Daniel McDonald", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/scripts/fix_arb_fasta.py b/scripts/fix_arb_fasta.py index ede2897011..41a8991079 100755 --- a/scripts/fix_arb_fasta.py +++ b/scripts/fix_arb_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/group_significance.py b/scripts/group_significance.py index f9372a08ca..b45e67c3fb 100755 --- a/scripts/group_significance.py +++ b/scripts/group_significance.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Jai Ram Rideout", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/identify_chimeric_seqs.py b/scripts/identify_chimeric_seqs.py index 1b6a705c37..a1ca6f7204 100755 --- a/scripts/identify_chimeric_seqs.py +++ b/scripts/identify_chimeric_seqs.py @@ -12,7 +12,7 @@ "Jens Reeder", "William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/identify_missing_files.py b/scripts/identify_missing_files.py index bc1b495931..8dee2139ca 100755 --- a/scripts/identify_missing_files.py +++ b/scripts/identify_missing_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/identify_paired_differences.py b/scripts/identify_paired_differences.py index e2366925b0..6f6e53eba9 100755 --- a/scripts/identify_paired_differences.py +++ b/scripts/identify_paired_differences.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/inflate_denoiser_output.py b/scripts/inflate_denoiser_output.py index 55003bb031..a3872a42fa 100755 --- a/scripts/inflate_denoiser_output.py +++ b/scripts/inflate_denoiser_output.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/jackknifed_beta_diversity.py b/scripts/jackknifed_beta_diversity.py index ddea202cc3..ae143a87a9 100755 --- a/scripts/jackknifed_beta_diversity.py +++ b/scripts/jackknifed_beta_diversity.py @@ -9,7 +9,7 @@ "Justin Kuczynski", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/join_paired_ends.py b/scripts/join_paired_ends.py index 6f648bcca7..ac3c7ee162 100755 --- a/scripts/join_paired_ends.py +++ b/scripts/join_paired_ends.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/scripts/load_remote_mapping_file.py b/scripts/load_remote_mapping_file.py index 63e07de4bf..50a7f8f616 100755 --- a/scripts/load_remote_mapping_file.py +++ b/scripts/load_remote_mapping_file.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_2d_plots.py b/scripts/make_2d_plots.py index c974b1b1ea..8bb730e3bc 100755 --- a/scripts/make_2d_plots.py +++ b/scripts/make_2d_plots.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina", "John Chase"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_bipartite_network.py b/scripts/make_bipartite_network.py index 7e45059eee..2a04d35f3d 100755 --- a/scripts/make_bipartite_network.py +++ b/scripts/make_bipartite_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren, Julia Goodrich, Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/make_bootstrapped_tree.py b/scripts/make_bootstrapped_tree.py index 71c7a380eb..cec93cff9c 100755 --- a/scripts/make_bootstrapped_tree.py +++ b/scripts/make_bootstrapped_tree.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/make_distance_boxplots.py b/scripts/make_distance_boxplots.py index 9b58517a8e..a4d29b9fff 100755 --- a/scripts/make_distance_boxplots.py +++ b/scripts/make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_distance_comparison_plots.py b/scripts/make_distance_comparison_plots.py index e66518f524..bf7be55b12 100755 --- a/scripts/make_distance_comparison_plots.py +++ b/scripts/make_distance_comparison_plots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_fastq.py b/scripts/make_fastq.py index 4e959d3216..204ccc4ece 100755 --- a/scripts/make_fastq.py +++ b/scripts/make_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_library_id_lists.py b/scripts/make_library_id_lists.py index d5ebadd679..00119e3bd6 100755 --- a/scripts/make_library_id_lists.py +++ b/scripts/make_library_id_lists.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Doug Wendel"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_otu_heatmap.py b/scripts/make_otu_heatmap.py index ed99ca02c7..1bc44bbf49 100755 --- a/scripts/make_otu_heatmap.py +++ b/scripts/make_otu_heatmap.py @@ -10,7 +10,7 @@ "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/scripts/make_otu_network.py b/scripts/make_otu_network.py index 0953f71796..82426f229d 100755 --- a/scripts/make_otu_network.py +++ b/scripts/make_otu_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Julia Goodrich", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/scripts/make_otu_table.py b/scripts/make_otu_table.py index 0b00c1bb7c..0950623217 100755 --- a/scripts/make_otu_table.py +++ b/scripts/make_otu_table.py @@ -12,7 +12,7 @@ "Adam Robbins-Pianka", "Sami Pietila"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/make_per_library_sff.py b/scripts/make_per_library_sff.py index e262d53416..cab4229430 100755 --- a/scripts/make_per_library_sff.py +++ b/scripts/make_per_library_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Daniel McDonald", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_phylogeny.py b/scripts/make_phylogeny.py index 9729cf97e9..332d07f367 100755 --- a/scripts/make_phylogeny.py +++ b/scripts/make_phylogeny.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/make_prefs_file.py b/scripts/make_prefs_file.py index 632b12335b..595a8ef823 100755 --- a/scripts/make_prefs_file.py +++ b/scripts/make_prefs_file.py @@ -9,7 +9,7 @@ "Jeremy Widmann", "Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_qiime_py_file.py b/scripts/make_qiime_py_file.py index 7a79b51429..a496c92192 100755 --- a/scripts/make_qiime_py_file.py +++ b/scripts/make_qiime_py_file.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" @@ -88,7 +88,7 @@ def main(): __copyright__ = "COPYRIGHT" __credits__ = ["AUTHOR_NAME"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "AUTHOR_NAME" __email__ = "AUTHOR_EMAIL" """ % strftime('%d %b %Y') diff --git a/scripts/make_rarefaction_plots.py b/scripts/make_rarefaction_plots.py index 555aa03a78..e632616fb9 100755 --- a/scripts/make_rarefaction_plots.py +++ b/scripts/make_rarefaction_plots.py @@ -7,7 +7,7 @@ __credits__ = ["Meg Pirrung", "Jesse Stombaugh", "John Chase", "Jai Ram Rideout", "Evan Bolyen"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_tep.py b/scripts/make_tep.py index 04e6fbb976..26d2729830 100755 --- a/scripts/make_tep.py +++ b/scripts/make_tep.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Meg Pirrung", "Jesse Stombaugh", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Meg Pirrung" __email__ = "meganap@gmail.com" diff --git a/scripts/map_reads_to_reference.py b/scripts/map_reads_to_reference.py index d8946c9568..60e11a1cf3 100755 --- a/scripts/map_reads_to_reference.py +++ b/scripts/map_reads_to_reference.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_mapping_files.py b/scripts/merge_mapping_files.py index 3cc2d35846..8066aa1227 100755 --- a/scripts/merge_mapping_files.py +++ b/scripts/merge_mapping_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_otu_maps.py b/scripts/merge_otu_maps.py index c18979f485..f2b43b8502 100755 --- a/scripts/merge_otu_maps.py +++ b/scripts/merge_otu_maps.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_otu_tables.py b/scripts/merge_otu_tables.py index 78ff088d73..40c04c46d9 100755 --- a/scripts/merge_otu_tables.py +++ b/scripts/merge_otu_tables.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/multiple_extract_barcodes.py b/scripts/multiple_extract_barcodes.py index 5f06fe5be3..f1ab3a9582 100755 --- a/scripts/multiple_extract_barcodes.py +++ b/scripts/multiple_extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/multiple_join_paired_ends.py b/scripts/multiple_join_paired_ends.py index 7e9314468f..c59c21a55f 100755 --- a/scripts/multiple_join_paired_ends.py +++ b/scripts/multiple_join_paired_ends.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/multiple_rarefactions.py b/scripts/multiple_rarefactions.py index 82af3698e2..bb18181409 100755 --- a/scripts/multiple_rarefactions.py +++ b/scripts/multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/multiple_rarefactions_even_depth.py b/scripts/multiple_rarefactions_even_depth.py index 91e8957df6..7a5d39899d 100755 --- a/scripts/multiple_rarefactions_even_depth.py +++ b/scripts/multiple_rarefactions_even_depth.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/multiple_split_libraries_fastq.py b/scripts/multiple_split_libraries_fastq.py index b5bab93ca2..12bd47fe67 100755 --- a/scripts/multiple_split_libraries_fastq.py +++ b/scripts/multiple_split_libraries_fastq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/neighbor_joining.py b/scripts/neighbor_joining.py index 79a0c4057a..2060d65eaa 100755 --- a/scripts/neighbor_joining.py +++ b/scripts/neighbor_joining.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/nmds.py b/scripts/nmds.py index 3fde479fab..cabf08dec3 100755 --- a/scripts/nmds.py +++ b/scripts/nmds.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/normalize_table.py b/scripts/normalize_table.py index 110e09b0ed..05a016e821 100755 --- a/scripts/normalize_table.py +++ b/scripts/normalize_table.py @@ -11,7 +11,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/scripts/observation_metadata_correlation.py b/scripts/observation_metadata_correlation.py index eab5699128..28f199ca8b 100755 --- a/scripts/observation_metadata_correlation.py +++ b/scripts/observation_metadata_correlation.py @@ -6,7 +6,7 @@ "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/otu_category_significance.py b/scripts/otu_category_significance.py index 7dc2a2828b..a65de6000f 100755 --- a/scripts/otu_category_significance.py +++ b/scripts/otu_category_significance.py @@ -7,7 +7,7 @@ __credits__ = ["Catherine Lozupone", "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Doug Wendel" __email__ = "wendel@colorado.edu" diff --git a/scripts/parallel_align_seqs_pynast.py b/scripts/parallel_align_seqs_pynast.py index 936bc69924..81add08a52 100755 --- a/scripts/parallel_align_seqs_pynast.py +++ b/scripts/parallel_align_seqs_pynast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_alpha_diversity.py b/scripts/parallel_alpha_diversity.py index 941020d2dd..d12444fc34 100755 --- a/scripts/parallel_alpha_diversity.py +++ b/scripts/parallel_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_blast.py b/scripts/parallel_assign_taxonomy_blast.py index 9579b95f33..00213a3a81 100755 --- a/scripts/parallel_assign_taxonomy_blast.py +++ b/scripts/parallel_assign_taxonomy_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_rdp.py b/scripts/parallel_assign_taxonomy_rdp.py index 7e7499f0f9..8da2bb9205 100755 --- a/scripts/parallel_assign_taxonomy_rdp.py +++ b/scripts/parallel_assign_taxonomy_rdp.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena", "William Walters", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_uclust.py b/scripts/parallel_assign_taxonomy_uclust.py index d71e400fbb..23cccd599d 100755 --- a/scripts/parallel_assign_taxonomy_uclust.py +++ b/scripts/parallel_assign_taxonomy_uclust.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_beta_diversity.py b/scripts/parallel_beta_diversity.py index a4b4cf3907..508c92312f 100755 --- a/scripts/parallel_beta_diversity.py +++ b/scripts/parallel_beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_blast.py b/scripts/parallel_blast.py index 19a20ec828..7f871a3fd5 100755 --- a/scripts/parallel_blast.py +++ b/scripts/parallel_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_identify_chimeric_seqs.py b/scripts/parallel_identify_chimeric_seqs.py index 8c64291159..a8f1e85f4f 100755 --- a/scripts/parallel_identify_chimeric_seqs.py +++ b/scripts/parallel_identify_chimeric_seqs.py @@ -6,7 +6,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_map_reads_to_reference.py b/scripts/parallel_map_reads_to_reference.py index afd7c47800..3355c0518e 100755 --- a/scripts/parallel_map_reads_to_reference.py +++ b/scripts/parallel_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_merge_otu_tables.py b/scripts/parallel_merge_otu_tables.py index 07331f8a7d..be10f239c9 100755 --- a/scripts/parallel_merge_otu_tables.py +++ b/scripts/parallel_merge_otu_tables.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/parallel_multiple_rarefactions.py b/scripts/parallel_multiple_rarefactions.py index 70697d9ac9..bd6fc70113 100755 --- a/scripts/parallel_multiple_rarefactions.py +++ b/scripts/parallel_multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_blast.py b/scripts/parallel_pick_otus_blast.py index 35991fc2da..283905abea 100755 --- a/scripts/parallel_pick_otus_blast.py +++ b/scripts/parallel_pick_otus_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_sortmerna.py b/scripts/parallel_pick_otus_sortmerna.py index 4aad04ae83..2243ef43aa 100755 --- a/scripts/parallel_pick_otus_sortmerna.py +++ b/scripts/parallel_pick_otus_sortmerna.py @@ -2,7 +2,7 @@ from __future__ import division __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jenya Kopylov" __email__ = "jenya.kopylov@gmail.com" diff --git a/scripts/parallel_pick_otus_trie.py b/scripts/parallel_pick_otus_trie.py index be5423a419..54f5fae32a 100755 --- a/scripts/parallel_pick_otus_trie.py +++ b/scripts/parallel_pick_otus_trie.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/parallel_pick_otus_uclust_ref.py b/scripts/parallel_pick_otus_uclust_ref.py index 8f10a75662..6e3c075ba1 100755 --- a/scripts/parallel_pick_otus_uclust_ref.py +++ b/scripts/parallel_pick_otus_uclust_ref.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_usearch61_ref.py b/scripts/parallel_pick_otus_usearch61_ref.py index dc636aec38..7aa6e18719 100755 --- a/scripts/parallel_pick_otus_usearch61_ref.py +++ b/scripts/parallel_pick_otus_usearch61_ref.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_closed_reference_otus.py b/scripts/pick_closed_reference_otus.py index bc56ebf202..5aa9601a36 100755 --- a/scripts/pick_closed_reference_otus.py +++ b/scripts/pick_closed_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_de_novo_otus.py b/scripts/pick_de_novo_otus.py index 0c1d7da191..5184d9f15d 100755 --- a/scripts/pick_de_novo_otus.py +++ b/scripts/pick_de_novo_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_open_reference_otus.py b/scripts/pick_open_reference_otus.py index 049588b9f6..a4e29f6ccd 100755 --- a/scripts/pick_open_reference_otus.py +++ b/scripts/pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_otus.py b/scripts/pick_otus.py index 3bd334f2f4..beb4aff160 100755 --- a/scripts/pick_otus.py +++ b/scripts/pick_otus.py @@ -8,7 +8,7 @@ "Jens Reeder", "William Walters", "Jose Carlos Clemente Litran", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_rep_set.py b/scripts/pick_rep_set.py index 7cf2dfd7bb..8d95a63761 100755 --- a/scripts/pick_rep_set.py +++ b/scripts/pick_rep_set.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/scripts/plot_rank_abundance_graph.py b/scripts/plot_rank_abundance_graph.py index 67e8c564ef..0b25620a1a 100755 --- a/scripts/plot_rank_abundance_graph.py +++ b/scripts/plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/plot_semivariogram.py b/scripts/plot_semivariogram.py index 809db8a2c5..626a869928 100755 --- a/scripts/plot_semivariogram.py +++ b/scripts/plot_semivariogram.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Kyle Patnode", "Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/plot_taxa_summary.py b/scripts/plot_taxa_summary.py index 1c03e800ec..a35cea207f 100755 --- a/scripts/plot_taxa_summary.py +++ b/scripts/plot_taxa_summary.py @@ -7,7 +7,7 @@ __credits__ = ["Jesse Stombaugh", "Julia Goodrich", "Justin Kuczynski", "John Chase", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" """ diff --git a/scripts/poller.py b/scripts/poller.py index 57f462b7f6..644e6bd6fe 100755 --- a/scripts/poller.py +++ b/scripts/poller.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/principal_coordinates.py b/scripts/principal_coordinates.py index f14fd05ef2..b59babc6ce 100755 --- a/scripts/principal_coordinates.py +++ b/scripts/principal_coordinates.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Antonio Gonzalez Pena", "Catherine Lozupone", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/print_metadata_stats.py b/scripts/print_metadata_stats.py index 3c0ed3fa24..7149a7d69e 100755 --- a/scripts/print_metadata_stats.py +++ b/scripts/print_metadata_stats.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/print_qiime_config.py b/scripts/print_qiime_config.py index 4cd0fe9ad8..40cf58935b 100755 --- a/scripts/print_qiime_config.py +++ b/scripts/print_qiime_config.py @@ -7,7 +7,7 @@ "Justin Kuczynski", "Jai Ram Rideout", "Greg Caporaso", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_iseq.py b/scripts/process_iseq.py index 5577da3e3f..ce3eda8ff4 100755 --- a/scripts/process_iseq.py +++ b/scripts/process_iseq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_qseq.py b/scripts/process_qseq.py index ddfcb96c8f..f5ae7e6906 100755 --- a/scripts/process_qseq.py +++ b/scripts/process_qseq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_sff.py b/scripts/process_sff.py index 8076e92884..190fb6d804 100755 --- a/scripts/process_sff.py +++ b/scripts/process_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Kyle Bittinger", "Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/quality_scores_plot.py b/scripts/quality_scores_plot.py index f81a9b502c..53f7fb0e98 100755 --- a/scripts/quality_scores_plot.py +++ b/scripts/quality_scores_plot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/relatedness.py b/scripts/relatedness.py index a7f1de9b02..280715d7d5 100755 --- a/scripts/relatedness.py +++ b/scripts/relatedness.py @@ -8,7 +8,7 @@ "Jose Antonio Navas Molina", "Yoshiki Vazquez Baeza", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/shared_phylotypes.py b/scripts/shared_phylotypes.py index 6351530ec2..7eabd28016 100755 --- a/scripts/shared_phylotypes.py +++ b/scripts/shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/scripts/simsam.py b/scripts/simsam.py index f66834f2b0..ff02537a5b 100755 --- a/scripts/simsam.py +++ b/scripts/simsam.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/single_rarefaction.py b/scripts/single_rarefaction.py index 2c841014b2..b2a5bc80b5 100755 --- a/scripts/single_rarefaction.py +++ b/scripts/single_rarefaction.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/sort_otu_table.py b/scripts/sort_otu_table.py index f42e134c4b..2169b54be9 100755 --- a/scripts/sort_otu_table.py +++ b/scripts/sort_otu_table.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Daniel McDonald", "Emily TerAvest", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_libraries.py b/scripts/split_libraries.py index 4fc4d5ad93..fa58e97604 100755 --- a/scripts/split_libraries.py +++ b/scripts/split_libraries.py @@ -9,7 +9,7 @@ "Jens Reeder", "Jose Antonio Navas Molina", "Jai Ram Rideout"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/scripts/split_libraries_fastq.py b/scripts/split_libraries_fastq.py index 85b4cf1770..3b4e724c5a 100755 --- a/scripts/split_libraries_fastq.py +++ b/scripts/split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_libraries_lea_seq.py b/scripts/split_libraries_lea_seq.py index 3706a73a57..5696d169f8 100755 --- a/scripts/split_libraries_lea_seq.py +++ b/scripts/split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/scripts/split_otu_table.py b/scripts/split_otu_table.py index 406ff9b6d1..90487d0754 100755 --- a/scripts/split_otu_table.py +++ b/scripts/split_otu_table.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_otu_table_by_taxonomy.py b/scripts/split_otu_table_by_taxonomy.py index 9d43944b5b..88de2f3a35 100755 --- a/scripts/split_otu_table_by_taxonomy.py +++ b/scripts/split_otu_table_by_taxonomy.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2010, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_sequence_file_on_sample_ids.py b/scripts/split_sequence_file_on_sample_ids.py index 3f2ef29aa1..5b93bea841 100755 --- a/scripts/split_sequence_file_on_sample_ids.py +++ b/scripts/split_sequence_file_on_sample_ids.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs.py b/scripts/start_parallel_jobs.py index 4da5baf6b7..847fd83463 100755 --- a/scripts/start_parallel_jobs.py +++ b/scripts/start_parallel_jobs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs_sc.py b/scripts/start_parallel_jobs_sc.py index 072999468e..eb070a6538 100755 --- a/scripts/start_parallel_jobs_sc.py +++ b/scripts/start_parallel_jobs_sc.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs_slurm.py b/scripts/start_parallel_jobs_slurm.py index 7f7b88c4d5..ab58d3b894 100755 --- a/scripts/start_parallel_jobs_slurm.py +++ b/scripts/start_parallel_jobs_slurm.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Rob Knight", "Greg Caporaso", "Jai Ram Rideout", "Evan Bolyen", "Simon Jacobs"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Simon Jacobs" __email__ = "sdjacobs@uchicago.edu" diff --git a/scripts/start_parallel_jobs_torque.py b/scripts/start_parallel_jobs_torque.py index befe3c8eb6..db315836d2 100755 --- a/scripts/start_parallel_jobs_torque.py +++ b/scripts/start_parallel_jobs_torque.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Rob Knight", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/subsample_fasta.py b/scripts/subsample_fasta.py index 18c2d31d36..24000006ce 100755 --- a/scripts/subsample_fasta.py +++ b/scripts/subsample_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/summarize_taxa.py b/scripts/summarize_taxa.py index 9401ee0502..8d01f5f654 100755 --- a/scripts/summarize_taxa.py +++ b/scripts/summarize_taxa.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Jose Carlos Clemente Litran", "Greg Caporaso", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/scripts/summarize_taxa_through_plots.py b/scripts/summarize_taxa_through_plots.py index d80db4af99..4bc6255fc6 100755 --- a/scripts/summarize_taxa_through_plots.py +++ b/scripts/summarize_taxa_through_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/supervised_learning.py b/scripts/supervised_learning.py index 10a7fcd6f3..a7cfca28cf 100755 --- a/scripts/supervised_learning.py +++ b/scripts/supervised_learning.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/scripts/transform_coordinate_matrices.py b/scripts/transform_coordinate_matrices.py index b9ec7cfb78..e5930ce326 100755 --- a/scripts/transform_coordinate_matrices.py +++ b/scripts/transform_coordinate_matrices.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Jose Carlos Clemente Litran", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/tree_compare.py b/scripts/tree_compare.py index fec92750de..0f8b84b849 100755 --- a/scripts/tree_compare.py +++ b/scripts/tree_compare.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/trflp_file_to_otu_table.py b/scripts/trflp_file_to_otu_table.py index d57fb147b8..d456eebe14 100755 --- a/scripts/trflp_file_to_otu_table.py +++ b/scripts/trflp_file_to_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/trim_sff_primers.py b/scripts/trim_sff_primers.py index a77b115a38..e3a2473ad6 100755 --- a/scripts/trim_sff_primers.py +++ b/scripts/trim_sff_primers.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/truncate_fasta_qual_files.py b/scripts/truncate_fasta_qual_files.py index 2f98e38c54..455bf10889 100755 --- a/scripts/truncate_fasta_qual_files.py +++ b/scripts/truncate_fasta_qual_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/truncate_reverse_primer.py b/scripts/truncate_reverse_primer.py index 315251e351..c7580d0497 100755 --- a/scripts/truncate_reverse_primer.py +++ b/scripts/truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/unweight_fasta.py b/scripts/unweight_fasta.py index ecb1e7deaa..f047c4748d 100755 --- a/scripts/unweight_fasta.py +++ b/scripts/unweight_fasta.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/upgma_cluster.py b/scripts/upgma_cluster.py index c81db6499c..d9859104ed 100755 --- a/scripts/upgma_cluster.py +++ b/scripts/upgma_cluster.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/validate_demultiplexed_fasta.py b/scripts/validate_demultiplexed_fasta.py index 398e61aef4..94fef63383 100755 --- a/scripts/validate_demultiplexed_fasta.py +++ b/scripts/validate_demultiplexed_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/validate_mapping_file.py b/scripts/validate_mapping_file.py index 0da88a1c8f..e58e12169b 100755 --- a/scripts/validate_mapping_file.py +++ b/scripts/validate_mapping_file.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/setup.py b/setup.py index 347c8dd3a2..b4df58aae1 100644 --- a/setup.py +++ b/setup.py @@ -20,7 +20,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout", "Yoshiki Vazquez Baeza", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "qiime.help@gmail.com" diff --git a/tests/__init__.py b/tests/__init__.py index a6eef5d6cc..330b27b581 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -16,6 +16,6 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/all_tests.py b/tests/all_tests.py index 16d2c0ace5..5d5406fde1 100755 --- a/tests/all_tests.py +++ b/tests/all_tests.py @@ -17,7 +17,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_add_alpha_to_mapping_file.py b/tests/test_add_alpha_to_mapping_file.py index d0b6aba631..a8f0358572 100755 --- a/tests/test_add_alpha_to_mapping_file.py +++ b/tests/test_add_alpha_to_mapping_file.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/tests/test_add_qiime_labels.py b/tests/test_add_qiime_labels.py index e02ae2b482..65db11ecce 100755 --- a/tests/test_add_qiime_labels.py +++ b/tests/test_add_qiime_labels.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_adjust_seq_orientation.py b/tests/test_adjust_seq_orientation.py index 3abb8a7d69..88844e6817 100755 --- a/tests/test_adjust_seq_orientation.py +++ b/tests/test_adjust_seq_orientation.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_align_seqs.py b/tests/test_align_seqs.py index 69a1f9ca3f..5c92f5e814 100644 --- a/tests/test_align_seqs.py +++ b/tests/test_align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_alpha_diversity.py b/tests/test_alpha_diversity.py index 776d385ac4..db76217ffa 100644 --- a/tests/test_alpha_diversity.py +++ b/tests/test_alpha_diversity.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_assign_taxonomy.py b/tests/test_assign_taxonomy.py index a5f7e742df..b10155652b 100644 --- a/tests/test_assign_taxonomy.py +++ b/tests/test_assign_taxonomy.py @@ -8,7 +8,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "David Soergel", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_barcode.py b/tests/test_barcode.py index f3c1512741..af32e30f4c 100644 --- a/tests/test_barcode.py +++ b/tests/test_barcode.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Justin Kuczynski", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_beta_diversity.py b/tests/test_beta_diversity.py index 397302cb80..3f26906067 100644 --- a/tests/test_beta_diversity.py +++ b/tests/test_beta_diversity.py @@ -5,7 +5,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_beta_metrics.py b/tests/test_beta_metrics.py index 14e7231620..19a006b5f6 100644 --- a/tests/test_beta_metrics.py +++ b/tests/test_beta_metrics.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "justin kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_biplots.py b/tests/test_biplots.py index 4a1d6a36a2..aa5bf2a9fa 100755 --- a/tests/test_biplots.py +++ b/tests/test_biplots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_categorized_dist_scatterplot.py b/tests/test_categorized_dist_scatterplot.py index 375fee2593..6d373d0ba4 100755 --- a/tests/test_categorized_dist_scatterplot.py +++ b/tests/test_categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_clean_raxml_parsimony_tree.py b/tests/test_clean_raxml_parsimony_tree.py index bb1e718aa3..09f76f1285 100755 --- a/tests/test_clean_raxml_parsimony_tree.py +++ b/tests/test_clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_cluster_quality.py b/tests/test_cluster_quality.py index 7c47e85b55..7b9db5ea21 100644 --- a/tests/test_cluster_quality.py +++ b/tests/test_cluster_quality.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_collate_alpha.py b/tests/test_collate_alpha.py index 66acc27bd8..70a453096c 100644 --- a/tests/test_collate_alpha.py +++ b/tests/test_collate_alpha.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_colors.py b/tests/test_colors.py index 1fdd7c015f..94a292a41f 100644 --- a/tests/test_colors.py +++ b/tests/test_colors.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_compare_alpha_diversity.py b/tests/test_compare_alpha_diversity.py index 6c893d1121..d9c2cedfb8 100755 --- a/tests/test_compare_alpha_diversity.py +++ b/tests/test_compare_alpha_diversity.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/tests/test_compare_categories.py b/tests/test_compare_categories.py index 2e1bee3f1b..3cf9a32f84 100644 --- a/tests/test_compare_categories.py +++ b/tests/test_compare_categories.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_distance_matrices.py b/tests/test_compare_distance_matrices.py index b77d600819..4b2937d8ec 100644 --- a/tests/test_compare_distance_matrices.py +++ b/tests/test_compare_distance_matrices.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_taxa_summaries.py b/tests/test_compare_taxa_summaries.py index fcd962b828..0deff6c892 100644 --- a/tests/test_compare_taxa_summaries.py +++ b/tests/test_compare_taxa_summaries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_trajectories.py b/tests/test_compare_trajectories.py index 3bdd0bdb3c..ab1ccce227 100644 --- a/tests/test_compare_trajectories.py +++ b/tests/test_compare_trajectories.py @@ -6,7 +6,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/tests/test_compute_taxonomy_ratios.py b/tests/test_compute_taxonomy_ratios.py index c94d9c5c2a..ae2c4919c9 100644 --- a/tests/test_compute_taxonomy_ratios.py +++ b/tests/test_compute_taxonomy_ratios.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Daniel McDonald"] __license__ = "BSD" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/tests/test_convert_fastaqual_fastq.py b/tests/test_convert_fastaqual_fastq.py index be0baf9cdf..cd64c6044b 100755 --- a/tests/test_convert_fastaqual_fastq.py +++ b/tests/test_convert_fastaqual_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Adam Robbins-Pianka", "Abhisaar Yadav", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/tests/test_core_microbiome.py b/tests/test_core_microbiome.py index 11c24a19db..16a139cba3 100755 --- a/tests/test_core_microbiome.py +++ b/tests/test_core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_demultiplex_fasta.py b/tests/test_demultiplex_fasta.py index 49f2d65204..f1a1b10b88 100755 --- a/tests/test_demultiplex_fasta.py +++ b/tests/test_demultiplex_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_denoise_wrapper.py b/tests/test_denoise_wrapper.py index 6e02b5cce9..12055c9e54 100644 --- a/tests/test_denoise_wrapper.py +++ b/tests/test_denoise_wrapper.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_denoiser/test_cluster_util.py b/tests/test_denoiser/test_cluster_util.py index 3343b16e75..56296c82c2 100644 --- a/tests/test_denoiser/test_cluster_util.py +++ b/tests/test_denoiser/test_cluster_util.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_denoise_postprocess.py b/tests/test_denoiser/test_denoise_postprocess.py index 8126501774..fd2eb72710 100644 --- a/tests/test_denoiser/test_denoise_postprocess.py +++ b/tests/test_denoiser/test_denoise_postprocess.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_denoiser.py b/tests/test_denoiser/test_denoiser.py index 7a88d3e085..8777130d39 100644 --- a/tests/test_denoiser/test_denoiser.py +++ b/tests/test_denoiser/test_denoiser.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_flowgram_clustering.py b/tests/test_denoiser/test_flowgram_clustering.py index 3502255444..450d92a7ce 100644 --- a/tests/test_denoiser/test_flowgram_clustering.py +++ b/tests/test_denoiser/test_flowgram_clustering.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_flowgram_filter.py b/tests/test_denoiser/test_flowgram_filter.py index cf996824be..256293d758 100644 --- a/tests/test_denoiser/test_flowgram_filter.py +++ b/tests/test_denoiser/test_flowgram_filter.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_make_cluster_jobs.py b/tests/test_denoiser/test_make_cluster_jobs.py index a24489921f..fb9f23cfe6 100644 --- a/tests/test_denoiser/test_make_cluster_jobs.py +++ b/tests/test_denoiser/test_make_cluster_jobs.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_preprocess.py b/tests/test_denoiser/test_preprocess.py index 713b434da2..464c759883 100644 --- a/tests/test_denoiser/test_preprocess.py +++ b/tests/test_denoiser/test_preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_settings.py b/tests/test_denoiser/test_settings.py index c1b187a919..bee9ef8888 100644 --- a/tests/test_denoiser/test_settings.py +++ b/tests/test_denoiser/test_settings.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_utils.py b/tests/test_denoiser/test_utils.py index 97516b678f..2165281617 100644 --- a/tests/test_denoiser/test_utils.py +++ b/tests/test_denoiser/test_utils.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_detrend.py b/tests/test_detrend.py index e39d2a3d00..2c9f7e058c 100644 --- a/tests/test_detrend.py +++ b/tests/test_detrend.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_differential_abundance.py b/tests/test_differential_abundance.py index f011646a41..8498b7db17 100644 --- a/tests/test_differential_abundance.py +++ b/tests/test_differential_abundance.py @@ -15,7 +15,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/tests/test_distance_matrix_from_mapping.py b/tests/test_distance_matrix_from_mapping.py index bd05d81cf7..f4a4f82073 100644 --- a/tests/test_distance_matrix_from_mapping.py +++ b/tests/test_distance_matrix_from_mapping.py @@ -10,7 +10,7 @@ "Michael S. Robeson", ] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/tests/test_estimate_observation_richness.py b/tests/test_estimate_observation_richness.py index bee4d784bd..4d1352bec9 100644 --- a/tests/test_estimate_observation_richness.py +++ b/tests/test_estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_exclude_seqs_by_blast.py b/tests/test_exclude_seqs_by_blast.py index 20ab6e0f2b..b336c20a10 100644 --- a/tests/test_exclude_seqs_by_blast.py +++ b/tests/test_exclude_seqs_by_blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Zaneveld", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/tests/test_extract_barcodes.py b/tests/test_extract_barcodes.py index 21a44e5b23..8a64227c71 100644 --- a/tests/test_extract_barcodes.py +++ b/tests/test_extract_barcodes.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["William Walters", "Daniel McDonald"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_filter.py b/tests/test_filter.py index 038b4d66a7..3af2e4638b 100755 --- a/tests/test_filter.py +++ b/tests/test_filter.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_filter_alignment.py b/tests/test_filter_alignment.py index 42427eafe4..9b559bb46d 100755 --- a/tests/test_filter_alignment.py +++ b/tests/test_filter_alignment.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_filter_otus_by_sample.py b/tests/test_filter_otus_by_sample.py index 38156c81c8..bc951f4073 100644 --- a/tests/test_filter_otus_by_sample.py +++ b/tests/test_filter_otus_by_sample.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_format.py b/tests/test_format.py index d376f633de..354cd596e0 100755 --- a/tests/test_format.py +++ b/tests/test_format.py @@ -9,7 +9,7 @@ "Jai Ram Rideout", "Jose Antonio Navas Molina"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_golay.py b/tests/test_golay.py index 804e29cdb2..4e8011e756 100644 --- a/tests/test_golay.py +++ b/tests/test_golay.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_group.py b/tests/test_group.py index 1c7d1dd279..67d697594d 100755 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -8,7 +8,7 @@ "Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_hamming.py b/tests/test_hamming.py index 9563409b9a..5f6faa8943 100755 --- a/tests/test_hamming.py +++ b/tests/test_hamming.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Micah Hamady", "Rob Knight"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_hierarchical_cluster.py b/tests/test_hierarchical_cluster.py index ba0e366560..b87decccdb 100644 --- a/tests/test_hierarchical_cluster.py +++ b/tests/test_hierarchical_cluster.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_identify_chimeric_seqs.py b/tests/test_identify_chimeric_seqs.py index 4617a754e0..6f5eca60be 100755 --- a/tests/test_identify_chimeric_seqs.py +++ b/tests/test_identify_chimeric_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jens Reeder", "William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_join_paired_ends.py b/tests/test_join_paired_ends.py index 6c7a91668b..1f220f0e80 100644 --- a/tests/test_join_paired_ends.py +++ b/tests/test_join_paired_ends.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/tests/test_make_2d_plots.py b/tests/test_make_2d_plots.py index 26bd891f7e..796e1e7f4b 100644 --- a/tests/test_make_2d_plots.py +++ b/tests/test_make_2d_plots.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_make_bipartite_network.py b/tests/test_make_bipartite_network.py index bd77da0091..f6d230223e 100755 --- a/tests/test_make_bipartite_network.py +++ b/tests/test_make_bipartite_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/tests/test_make_bootstrapped_tree.py b/tests/test_make_bootstrapped_tree.py index 993eb5e4f2..948363730f 100644 --- a/tests/test_make_bootstrapped_tree.py +++ b/tests/test_make_bootstrapped_tree.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_make_distance_boxplots.py b/tests/test_make_distance_boxplots.py index cd1a4e8ca3..7f8a84bdae 100644 --- a/tests/test_make_distance_boxplots.py +++ b/tests/test_make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_make_fastq.py b/tests/test_make_fastq.py index 11e5715d70..fbc7d1b93e 100644 --- a/tests/test_make_fastq.py +++ b/tests/test_make_fastq.py @@ -9,7 +9,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_library_id_lists.py b/tests/test_make_library_id_lists.py index 974e679aed..a775caf8ee 100644 --- a/tests/test_make_library_id_lists.py +++ b/tests/test_make_library_id_lists.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_otu_heatmap.py b/tests/test_make_otu_heatmap.py index 86cab2cafa..1756b28a3e 100644 --- a/tests/test_make_otu_heatmap.py +++ b/tests/test_make_otu_heatmap.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_make_otu_network.py b/tests/test_make_otu_network.py index 19340ae468..a7874b93f1 100644 --- a/tests/test_make_otu_network.py +++ b/tests/test_make_otu_network.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Julia Goodrich", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/tests/test_make_otu_table.py b/tests/test_make_otu_table.py index 9681130541..582801bba9 100644 --- a/tests/test_make_otu_table.py +++ b/tests/test_make_otu_table.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight", "Justin Kuczynski", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_make_per_library_sff.py b/tests/test_make_per_library_sff.py index 83cf2d5379..28ebe1faf3 100644 --- a/tests/test_make_per_library_sff.py +++ b/tests/test_make_per_library_sff.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_phylogeny.py b/tests/test_make_phylogeny.py index 171be2a6de..b841aa2692 100644 --- a/tests/test_make_phylogeny.py +++ b/tests/test_make_phylogeny.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_make_rarefaction_plots.py b/tests/test_make_rarefaction_plots.py index 1316299e78..dfcffd3ed1 100755 --- a/tests/test_make_rarefaction_plots.py +++ b/tests/test_make_rarefaction_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_map_reads_to_reference.py b/tests/test_map_reads_to_reference.py index af301e4601..12bd07d1d2 100755 --- a/tests/test_map_reads_to_reference.py +++ b/tests/test_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_normalize_table.py b/tests/test_normalize_table.py index 14ed967a4c..10a9ae67af 100644 --- a/tests/test_normalize_table.py +++ b/tests/test_normalize_table.py @@ -16,7 +16,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/tests/test_otu_significance.py b/tests/test_otu_significance.py index abf9c751f4..c9a9db2d94 100755 --- a/tests/test_otu_significance.py +++ b/tests/test_otu_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Luke Ursell", "Will Van Treuren", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Luke Ursell" __email__ = "lkursell@gmail.com" diff --git a/tests/test_parallel/test_align_seqs.py b/tests/test_parallel/test_align_seqs.py index 035d730e7f..344e2e27e0 100755 --- a/tests/test_parallel/test_align_seqs.py +++ b/tests/test_parallel/test_align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_alpha_diversity.py b/tests/test_parallel/test_alpha_diversity.py index 676ff2855b..89b8dbcdff 100755 --- a/tests/test_parallel/test_alpha_diversity.py +++ b/tests/test_parallel/test_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_assign_taxonomy.py b/tests/test_parallel/test_assign_taxonomy.py index 424fb4a22f..ae074cde98 100755 --- a/tests/test_parallel/test_assign_taxonomy.py +++ b/tests/test_parallel/test_assign_taxonomy.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_beta_diversity.py b/tests/test_parallel/test_beta_diversity.py index ba82cd94df..c835933be0 100755 --- a/tests/test_parallel/test_beta_diversity.py +++ b/tests/test_parallel/test_beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_blast.py b/tests/test_parallel/test_blast.py index b67063ab77..4da6b3fd61 100755 --- a/tests/test_parallel/test_blast.py +++ b/tests/test_parallel/test_blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_identify_chimeric_seqs.py b/tests/test_parallel/test_identify_chimeric_seqs.py index 1e3dc7eb8c..b2ce9feaeb 100755 --- a/tests/test_parallel/test_identify_chimeric_seqs.py +++ b/tests/test_parallel/test_identify_chimeric_seqs.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_map_reads_to_reference.py b/tests/test_parallel/test_map_reads_to_reference.py index 96da693096..e21f9190ca 100755 --- a/tests/test_parallel/test_map_reads_to_reference.py +++ b/tests/test_parallel/test_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_merge_otus.py b/tests/test_parallel/test_merge_otus.py index d3f3650490..0ab20e176f 100644 --- a/tests/test_parallel/test_merge_otus.py +++ b/tests/test_parallel/test_merge_otus.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/tests/test_parallel/test_multiple_rarefactions.py b/tests/test_parallel/test_multiple_rarefactions.py index 50698f6927..95e882a0de 100755 --- a/tests/test_parallel/test_multiple_rarefactions.py +++ b/tests/test_parallel/test_multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_pick_otus.py b/tests/test_parallel/test_pick_otus.py index 7164c73000..01d31068dd 100755 --- a/tests/test_parallel/test_pick_otus.py +++ b/tests/test_parallel/test_pick_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_util.py b/tests/test_parallel/test_util.py index a17f46d453..7fd6482f1d 100755 --- a/tests/test_parallel/test_util.py +++ b/tests/test_parallel/test_util.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parse.py b/tests/test_parse.py index f540850617..48a3e15e2e 100644 --- a/tests/test_parse.py +++ b/tests/test_parse.py @@ -8,7 +8,7 @@ "Jai Ram Rideout", "Will Van Treuren", "Yoshiki Vazquez-Baeza", "Jose Antonio Navas Molina"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_pick_otus.py b/tests/test_pick_otus.py index 6fa17290ed..290383b527 100755 --- a/tests/test_pick_otus.py +++ b/tests/test_pick_otus.py @@ -13,7 +13,7 @@ "William Walters", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_pick_rep_set.py b/tests/test_pick_rep_set.py index c3fb1b55ce..c54f7da824 100644 --- a/tests/test_pick_rep_set.py +++ b/tests/test_pick_rep_set.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight", "Kyle Bittinger", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/tests/test_plot_rank_abundance_graph.py b/tests/test_plot_rank_abundance_graph.py index 4853f1eaeb..05dc463fe5 100755 --- a/tests/test_plot_rank_abundance_graph.py +++ b/tests/test_plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_plot_semivariogram.py b/tests/test_plot_semivariogram.py index 1519d820cc..e7d37da6e2 100644 --- a/tests/test_plot_semivariogram.py +++ b/tests/test_plot_semivariogram.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/tests/test_plot_taxa_summary.py b/tests/test_plot_taxa_summary.py index 5bbd021686..2df5b03094 100644 --- a/tests/test_plot_taxa_summary.py +++ b/tests/test_plot_taxa_summary.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh", "Julia Goodrich"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_principal_coordinates.py b/tests/test_principal_coordinates.py index 8e0a7ad083..e4a361bf50 100644 --- a/tests/test_principal_coordinates.py +++ b/tests/test_principal_coordinates.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_process_sff.py b/tests/test_process_sff.py index 8e127b85d1..5b5e014ac1 100644 --- a/tests/test_process_sff.py +++ b/tests/test_process_sff.py @@ -25,7 +25,7 @@ "Jesse Stombaugh", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_quality_scores_plot.py b/tests/test_quality_scores_plot.py index 1e3b5d0f29..247a007e98 100755 --- a/tests/test_quality_scores_plot.py +++ b/tests/test_quality_scores_plot.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_rarefaction.py b/tests/test_rarefaction.py index fb91694ebb..f9e37e1b75 100644 --- a/tests/test_rarefaction.py +++ b/tests/test_rarefaction.py @@ -5,7 +5,7 @@ __credits__ = ["justin kuczynski", "Rob Knight", "Jose Carlos Clemente Litran", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_relatedness.py b/tests/test_relatedness.py index 787666cffd..1774180d6f 100644 --- a/tests/test_relatedness.py +++ b/tests/test_relatedness.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/tests/test_remote.py b/tests/test_remote.py index 41ecfd7a59..e6de20cdfe 100644 --- a/tests/test_remote.py +++ b/tests/test_remote.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_shared_phylotypes.py b/tests/test_shared_phylotypes.py index 085687414a..1dc9d50735 100644 --- a/tests/test_shared_phylotypes.py +++ b/tests/test_shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/tests/test_simsam.py b/tests/test_simsam.py index bb594ed766..ee747fc34e 100755 --- a/tests/test_simsam.py +++ b/tests/test_simsam.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kucyznski", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kucyznski" __email__ = "justinak@gmail.com" diff --git a/tests/test_sort.py b/tests/test_sort.py index 1b723737ca..379075cbf5 100755 --- a/tests/test_sort.py +++ b/tests/test_sort.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split.py b/tests/test_split.py index 0e50212c88..8821c030ee 100755 --- a/tests/test_split.py +++ b/tests/test_split.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split_libraries.py b/tests/test_split_libraries.py index 83b2f70e50..c04496f749 100644 --- a/tests/test_split_libraries.py +++ b/tests/test_split_libraries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_split_libraries_fastq.py b/tests/test_split_libraries_fastq.py index 41b3813db6..439945e5f0 100755 --- a/tests/test_split_libraries_fastq.py +++ b/tests/test_split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split_libraries_lea_seq.py b/tests/test_split_libraries_lea_seq.py index 88116c5d1c..9a36ee989b 100644 --- a/tests/test_split_libraries_lea_seq.py +++ b/tests/test_split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/tests/test_stats.py b/tests/test_stats.py index fce4bf451a..351e71d0dd 100644 --- a/tests/test_stats.py +++ b/tests/test_stats.py @@ -7,7 +7,7 @@ "Damien Coy", "Levi McCracken", "Andrew Cochran", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_summarize_taxa.py b/tests/test_summarize_taxa.py index fd8a0734a1..3186fe7c67 100644 --- a/tests/test_summarize_taxa.py +++ b/tests/test_summarize_taxa.py @@ -11,7 +11,7 @@ "Antonio Gonzalez Pena", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/tests/test_supervised_learning.py b/tests/test_supervised_learning.py index aa4deeb8f5..0b87db3344 100644 --- a/tests/test_supervised_learning.py +++ b/tests/test_supervised_learning.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Dan Knights", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_transform_coordinate_matrices.py b/tests/test_transform_coordinate_matrices.py index b439695d50..8476777d49 100755 --- a/tests/test_transform_coordinate_matrices.py +++ b/tests/test_transform_coordinate_matrices.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_tree_compare.py b/tests/test_tree_compare.py index 3e2697dc85..4e93612623 100644 --- a/tests/test_tree_compare.py +++ b/tests/test_tree_compare.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_trim_sff_primers.py b/tests/test_trim_sff_primers.py index c7f32ae6ec..43658af60e 100644 --- a/tests/test_trim_sff_primers.py +++ b/tests/test_trim_sff_primers.py @@ -10,7 +10,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight", 'Kyle Bittinger'] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_truncate_fasta_qual_files.py b/tests/test_truncate_fasta_qual_files.py index 83b494908e..faa6202c5b 100755 --- a/tests/test_truncate_fasta_qual_files.py +++ b/tests/test_truncate_fasta_qual_files.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_truncate_reverse_primer.py b/tests/test_truncate_reverse_primer.py index 20bfac141b..cd621c3c23 100755 --- a/tests/test_truncate_reverse_primer.py +++ b/tests/test_truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_util.py b/tests/test_util.py index d1d7f59110..d00dbc9111 100755 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -69,7 +69,7 @@ "Levi McCracken", "Damien Coy", "Yoshiki Vazquez Baeza", "Will Van Treuren", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_validate_demultiplexed_fasta.py b/tests/test_validate_demultiplexed_fasta.py index 4d0374b8be..1e2a6f2ee6 100755 --- a/tests/test_validate_demultiplexed_fasta.py +++ b/tests/test_validate_demultiplexed_fasta.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/tests/test_validate_mapping_file.py b/tests/test_validate_mapping_file.py index f10c3a0fdb..99a99d35d9 100755 --- a/tests/test_validate_mapping_file.py +++ b/tests/test_validate_mapping_file.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_workflow/test_ampliconnoise.py b/tests/test_workflow/test_ampliconnoise.py index c72a337858..8a659f3c35 100755 --- a/tests/test_workflow/test_ampliconnoise.py +++ b/tests/test_workflow/test_ampliconnoise.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_core_diversity_analyses.py b/tests/test_workflow/test_core_diversity_analyses.py index 0d1ec8431e..059d7fa69f 100755 --- a/tests/test_workflow/test_core_diversity_analyses.py +++ b/tests/test_workflow/test_core_diversity_analyses.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_downstream.py b/tests/test_workflow/test_downstream.py index fb48429b55..a96d64ce18 100755 --- a/tests/test_workflow/test_downstream.py +++ b/tests/test_workflow/test_downstream.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_pick_open_reference_otus.py b/tests/test_workflow/test_pick_open_reference_otus.py index 9ad4b4c24e..cee01ab565 100755 --- a/tests/test_workflow/test_pick_open_reference_otus.py +++ b/tests/test_workflow/test_pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_preprocess.py b/tests/test_workflow/test_preprocess.py index d021c6e8f4..dc06994a88 100755 --- a/tests/test_workflow/test_preprocess.py +++ b/tests/test_workflow/test_preprocess.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_workflow/test_upstream.py b/tests/test_workflow/test_upstream.py index d51a42b4d3..33949307f0 100755 --- a/tests/test_workflow/test_upstream.py +++ b/tests/test_workflow/test_upstream.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_util.py b/tests/test_workflow/test_util.py index a8d67de278..dc9d067119 100755 --- a/tests/test_workflow/test_util.py +++ b/tests/test_workflow/test_util.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-dev" +__version__ = "1.9.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" From f0c598b88fc658d7098c116679e80eeb34482b78 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 22 May 2015 15:49:41 -0700 Subject: [PATCH 4/7] MAINT: fixed some broken links in the docs --- doc/tutorials/otu_picking.rst | 2 +- doc/tutorials/predicting_mislabeled_samples.rst | 2 +- doc/tutorials/procrustes_analysis.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/tutorials/otu_picking.rst b/doc/tutorials/otu_picking.rst index d3c32afde2..f012c0be18 100644 --- a/doc/tutorials/otu_picking.rst +++ b/doc/tutorials/otu_picking.rst @@ -8,7 +8,7 @@ QIIME provides three high-level protocols for OTU picking. These can be describe **Open-reference OTU picking with** ``pick_open_reference_otus.py`` **is the preferred strategy for OTU picking among the QIIME developers.** -.. note:: QIIME does not actually implement OTU picking algorithms, but rather wraps external OTU clustering tools. For this reason, it is important to cite the OTU clustering tools that you used directly, in addition to citing QIIME. There are a number of OTU clustering tools available through QIIME's workflows, including open source (e.g., `SortMeRNA `_, `SUMACLUST `_, and `swarm `_) and closed source tools (e.g., `uclust and usearch `_). ``uclust`` is the default OTU clustering tool used in QIIME's workflows. We are currently evaluating changing the default OTU clustering tool to one of the open source alternatives for future versions of QIIME. +.. note:: QIIME does not actually implement OTU picking algorithms, but rather wraps external OTU clustering tools. For this reason, it is important to cite the OTU clustering tools that you used directly, in addition to citing QIIME. There are a number of OTU clustering tools available through QIIME's workflows, including open source (e.g., `SortMeRNA `_, `SUMACLUST `_, and `swarm `_) and closed source tools (e.g., `uclust and usearch `_). ``uclust`` is the default OTU clustering tool used in QIIME's workflows. We are currently evaluating changing the default OTU clustering tool to one of the open source alternatives for future versions of QIIME. Description of QIIME's OTU picking protocols ============================================ diff --git a/doc/tutorials/predicting_mislabeled_samples.rst b/doc/tutorials/predicting_mislabeled_samples.rst index d72a01d4c7..b3d4e00cb3 100644 --- a/doc/tutorials/predicting_mislabeled_samples.rst +++ b/doc/tutorials/predicting_mislabeled_samples.rst @@ -27,7 +27,7 @@ One of the output files from :file:`supervised_learning.py` is the file :file:`m Visualizing mislabeled samples ------------------------------------------------------------------- -You can also visualize the predicted mislabels using `make_emperor.py `_. Assuming that you have run :file:`beta_diversity.py` and :file:`principal_coordinates.py` to obtain a principal coordinates table :file:`pcoa.txt` for your samples, you can use the following command to obtain a plot where samples are colored by their mislabeling status:: +You can also visualize the predicted mislabels using `make_emperor.py `_. Assuming that you have run :file:`beta_diversity.py` and :file:`principal_coordinates.py` to obtain a principal coordinates table :file:`pcoa.txt` for your samples, you can use the following command to obtain a plot where samples are colored by their mislabeling status:: make_emperor.py -i pcoa.txt -m ml/mislabeling.txt -o color_by_mislabeling diff --git a/doc/tutorials/procrustes_analysis.rst b/doc/tutorials/procrustes_analysis.rst index 63e1c7f6ec..84e0e29f22 100644 --- a/doc/tutorials/procrustes_analysis.rst +++ b/doc/tutorials/procrustes_analysis.rst @@ -4,7 +4,7 @@ Performing Procrustes Analysis ============================== -This tutorial covers how to perform Procrustes Analysis (`Gower (1975) `_) using QIIME to compare weighted and unweighted UniFrac PCoA plots generated by the same processing pipeline. Procrustes analysis takes as input two coordinate matrices with corresponding points (in QIIME, these are generated by running ``principal_coordinates.py`` on a distance matrix generated by ``beta_diversity.py``), and transforming the second coordinate set by rotating, scaling, and translating it to minimize the distances between corresponding points in the two shapes. This is done with ``transform_coordinate_matrices.py``. The results can then be visualized using QIIME by running `make_emperor.py `_ and using the ``-c/--compare_plots`` option. Both sets of coordinates will be plotted in the resulting figure, with bars connecting the corresponding points from each data set. +This tutorial covers how to perform Procrustes Analysis (`Gower (1975) `_) using QIIME to compare weighted and unweighted UniFrac PCoA plots generated by the same processing pipeline. Procrustes analysis takes as input two coordinate matrices with corresponding points (in QIIME, these are generated by running ``principal_coordinates.py`` on a distance matrix generated by ``beta_diversity.py``), and transforming the second coordinate set by rotating, scaling, and translating it to minimize the distances between corresponding points in the two shapes. This is done with ``transform_coordinate_matrices.py``. The results can then be visualized using QIIME by running `make_emperor.py `_ and using the ``-c/--compare_plots`` option. Both sets of coordinates will be plotted in the resulting figure, with bars connecting the corresponding points from each data set. Procrustes analysis allows us to determine whether we would derive the same beta diversity conclusions, regardless of which metric was used to compare the samples. This tutorial illustrates the steps used to generate this plot, beginning with the weighted and unweighted UniFrac PCoA matrices generated in the `Illumina Overview Tutorial <./illumina_overview_tutorial.html>`_. A similar analysis comparing 454 and Illumina sequencing of the same samples was presented in Supplementary Figure 1 of `Moving Pictures of the Human Microbiome `_. From fc5ef4668c1f2f683cbc19ebc357325673039192 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 22 May 2015 16:01:54 -0700 Subject: [PATCH 5/7] MAINT: fixed typo --- ChangeLog.md | 2 +- doc/scripts/jackknifed_beta_diversity.rst | 2 +- doc/tutorials/working_with_biom_tables.rst | 2 +- qiime/workflow/core_diversity_analyses.py | 14 +++++++------- qiime/workflow/downstream.py | 2 +- scripts/jackknifed_beta_diversity.py | 2 +- tests/test_workflow/test_downstream.py | 8 ++++---- 7 files changed, 16 insertions(+), 16 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index d146dcf84a..c4ed7fe4ea 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -24,7 +24,7 @@ Usability enhancements * If ``temp_dir`` is not defined in the QIIME config file, QIIME will use the system's default temporary directory instead of assuming that ``/tmp`` is present and writeable. Note that the location of this default temporary directory [can be changed with environment variables](https://docs.python.org/2/library/tempfile.html#tempfile.tempdir) ([#1995](https://github.com/biocore/qiime/issues/1995)). * Improve error reporting from ``filter_taxa_from_otu_table.py``, ``filter_otus_from_otu_table.py``, and ``filter_samples_from_otu_table.py`` when all OTUs/samples are filtered out resulting in an empty table ([#1963](https://github.com/biocore/qiime/issues/1963)), and generally when attempting to write an empty BIOM table from QIIME. * Added ability to pass user-defined runtime limit for jobs to ``start_parallel_jobs_slurm.py``. This can be achieved by setting the ``slurm_time`` variable in ``qiime_config``, or by passing ``--time`` to ``start_parallel_jobs_slurm.py``. -* Distances matrices and UPGMA trees generated from the full (unrarified) OTU table are now stored under ``unrarified_bdiv`` in the output directory from ``jackknifed_beta_diversity.py``. That UPGMA tree is optionally used (if the user passes ``--master_tree full``). This change makes their content more explicit so they're less likely to be used by accident ([#2024](https://github.com/biocore/qiime/issues/2024)). +* Distances matrices and UPGMA trees generated from the full (unrarefied) OTU table are now stored under ``unrarefied_bdiv`` in the output directory from ``jackknifed_beta_diversity.py``. That UPGMA tree is optionally used (if the user passes ``--master_tree full``). This change makes their content more explicit so they're less likely to be used by accident ([#2024](https://github.com/biocore/qiime/issues/2024)). QIIME 1.9.0 =========== diff --git a/doc/scripts/jackknifed_beta_diversity.rst b/doc/scripts/jackknifed_beta_diversity.rst index 96d0943b5b..550fadd069 100644 --- a/doc/scripts/jackknifed_beta_diversity.rst +++ b/doc/scripts/jackknifed_beta_diversity.rst @@ -48,7 +48,7 @@ To directly measure the robustness of individual UPGMA clusters and clusters in **Output:** -This scripts results in several distance matrices (from `beta_diversity.py <./beta_diversity.html>`_), several rarified OTU tables (from `multiple_rarefactions_even_depth.py <./multiple_rarefactions_even_depth.html>`_), several UPGMA trees (from `upgma_cluster.py <./upgma_cluster.html>`_), a supporting file and newick tree with support values (from `tree_compare.py <./tree_compare.html>`_), and Emperor PCoA plots. +This scripts results in several distance matrices (from `beta_diversity.py <./beta_diversity.html>`_), several rarefied OTU tables (from `multiple_rarefactions_even_depth.py <./multiple_rarefactions_even_depth.html>`_), several UPGMA trees (from `upgma_cluster.py <./upgma_cluster.html>`_), a supporting file and newick tree with support values (from `tree_compare.py <./tree_compare.html>`_), and Emperor PCoA plots. **Example:** diff --git a/doc/tutorials/working_with_biom_tables.rst b/doc/tutorials/working_with_biom_tables.rst index 79ed58160a..9c3cdcd6f9 100644 --- a/doc/tutorials/working_with_biom_tables.rst +++ b/doc/tutorials/working_with_biom_tables.rst @@ -14,7 +14,7 @@ Filtering Even sampling (rarefaction) --------------------------- -The `single_rarefaction.py <../scripts/single_rarefaction.html>`_ script allows the user to randomly subsample each of their samples to an equal count. This is essential for many diversity analyses, which assume that the count of observations for each sample is equal. `multiple_rarefactions.py <../scripts/multiple_rarefactions.html>`_ is a variant on this script which allows the user to generate rarified OTU tables at a range of different sampling depths (it is the equivalent of running `single_rarefaction.py <../scripts/single_rarefaction.html>`_ multiple times at different depths). `multiple_rarefactions_even_depth.py <../scripts/multiple_rarefactions_even_depth.html>`_ is another variant which allows the user to create many replicate subsampled OTU tables at a single depth. +The `single_rarefaction.py <../scripts/single_rarefaction.html>`_ script allows the user to randomly subsample each of their samples to an equal count. This is essential for many diversity analyses, which assume that the count of observations for each sample is equal. `multiple_rarefactions.py <../scripts/multiple_rarefactions.html>`_ is a variant on this script which allows the user to generate rarefied OTU tables at a range of different sampling depths (it is the equivalent of running `single_rarefaction.py <../scripts/single_rarefaction.html>`_ multiple times at different depths). `multiple_rarefactions_even_depth.py <../scripts/multiple_rarefactions_even_depth.html>`_ is another variant which allows the user to create many replicate subsampled OTU tables at a single depth. Filtering observations/OTUs ----------------------------- diff --git a/qiime/workflow/core_diversity_analyses.py b/qiime/workflow/core_diversity_analyses.py index a95f953412..195bcb6252 100644 --- a/qiime/workflow/core_diversity_analyses.py +++ b/qiime/workflow/core_diversity_analyses.py @@ -478,17 +478,17 @@ def run_core_diversity_analyses( filtered_biom_gzip_fp, _index_headers['run_summary'])) - rarified_biom_gzip_fp = '%s.gz' % rarefied_biom_fp - if not exists(rarified_biom_gzip_fp): + rarefied_biom_gzip_fp = '%s.gz' % rarefied_biom_fp + if not exists(rarefied_biom_gzip_fp): commands.append( - [('Compress the rarified BIOM table', 'gzip %s' % + [('Compress the rarefied BIOM table', 'gzip %s' % rarefied_biom_fp)]) else: - logger.write("Skipping compressing of rarified BIOM table as %s exists.\n\n" - % rarified_biom_gzip_fp) + logger.write("Skipping compressing of rarefied BIOM table as %s exists.\n\n" + % rarefied_biom_gzip_fp) index_links.append( - ('Rarified BIOM table (sampling depth: %d)' % sampling_depth, - rarified_biom_gzip_fp, + ('rarefied BIOM table (sampling depth: %d)' % sampling_depth, + rarefied_biom_gzip_fp, _index_headers['run_summary'])) if len(commands) > 0: diff --git a/qiime/workflow/downstream.py b/qiime/workflow/downstream.py index 3785638349..e5678b6ea8 100644 --- a/qiime/workflow/downstream.py +++ b/qiime/workflow/downstream.py @@ -398,7 +398,7 @@ def run_jackknifed_beta_diversity(otu_table_fp, beta_diversity_metrics = ['weighted_unifrac', 'unweighted_unifrac'] # Prep the beta-diversity command - full_table_bdiv_dir = join(output_dir, 'unrarified_bdiv') + full_table_bdiv_dir = join(output_dir, 'unrarefied_bdiv') try: params_str = get_params_str(params['beta_diversity']) except KeyError: diff --git a/scripts/jackknifed_beta_diversity.py b/scripts/jackknifed_beta_diversity.py index ae143a87a9..6770ebf71f 100755 --- a/scripts/jackknifed_beta_diversity.py +++ b/scripts/jackknifed_beta_diversity.py @@ -55,7 +55,7 @@ script_info['script_usage_output_to_remove'] = ['bdiv_jk100'] script_info['output_description'] = """This scripts results in several distance\ - matrices (from beta_diversity.py), several rarified OTU tables\ + matrices (from beta_diversity.py), several rarefied OTU tables\ (from multiple_rarefactions_even_depth.py), several UPGMA trees (from upgma_cluster.py),\ a supporting file and newick tree with support values (from tree_compare.py),\ and Emperor PCoA plots.""" diff --git a/tests/test_workflow/test_downstream.py b/tests/test_workflow/test_downstream.py index a96d64ce18..c7df404e2c 100755 --- a/tests/test_workflow/test_downstream.py +++ b/tests/test_workflow/test_downstream.py @@ -401,9 +401,9 @@ def test_run_jackknifed_beta_diversity(self): 'index.html') input_file_basename = splitext(split(self.test_data['biom'][0])[1])[0] - unweighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', + unweighted_unifrac_dm_fp = join(self.test_out, 'unrarefied_bdiv', 'unweighted_unifrac_%s.txt' % input_file_basename) - weighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', + weighted_unifrac_dm_fp = join(self.test_out, 'unrarefied_bdiv', 'weighted_unifrac_%s.txt' % input_file_basename) # check for expected relations between values in the unweighted unifrac @@ -460,9 +460,9 @@ def test_run_jackknifed_beta_diversity_parallel(self): 'index.html') input_file_basename = splitext(split(self.test_data['biom'][0])[1])[0] - unweighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', + unweighted_unifrac_dm_fp = join(self.test_out, 'unrarefied_bdiv', 'unweighted_unifrac_%s.txt' % input_file_basename) - weighted_unifrac_dm_fp = join(self.test_out, 'unrarified_bdiv', + weighted_unifrac_dm_fp = join(self.test_out, 'unrarefied_bdiv', 'weighted_unifrac_%s.txt' % input_file_basename) # check for expected relations between values in the unweighted unifrac From 269b5e1f01365dd60abebbb6959039bc7806064a Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 22 May 2015 16:25:35 -0700 Subject: [PATCH 6/7] REL: further clarified which bug fixes are critical --- ChangeLog.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index c4ed7fe4ea..15a75a7bd3 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -4,9 +4,9 @@ QIIME 1.9.1 Bug fixes --------- -* Updated minimum required version of the [qiime-default-reference](http://github.com/biocore/qiime-default-reference) package to 0.1.2. **This release includes an important bug fix described in more detail in [this QIIME blog post](https://qiime.wordpress.com/2015/04/15/qiime-1-9-0-bug-affecting-pynast-alignment-of-16s-amplicons-generated-with-non-515f806r-primers/) and in [biocore/qiime-default-reference#14](https://github.com/biocore/qiime-default-reference/issues/14).** -* Fixed bug in ``differential_abundance.py`` fitZIG algorithm ([#1960](https://github.com/biocore/qiime/pull/1960)). **This was a serious bug that was encountered when users would call ``differential_abundance.py -a metagenomeSeq_fitZIG``. Any results previosuly generated with that command should be re-run.** -* Fixed serious bug in ``observation_metadata_correlation.py``, described in [#2009](https://github.com/biocore/qiime/issues/2009). **All previous output generated with ``observation_metadata_correlation.py`` was incorrect, and analyses using those results should be re-run.** This most commonly would have resulted in massive Type 2 error (false negatives), where observations whose abundance is correlated with metadata are not reported, though Type 1 error (false positives) are also possible. +* **Critical**: Updated minimum required version of the [qiime-default-reference](http://github.com/biocore/qiime-default-reference) package to 0.1.2. **This release includes an important bug fix described in more detail in [this QIIME blog post](https://qiime.wordpress.com/2015/04/15/qiime-1-9-0-bug-affecting-pynast-alignment-of-16s-amplicons-generated-with-non-515f806r-primers/) and in [biocore/qiime-default-reference#14](https://github.com/biocore/qiime-default-reference/issues/14).** +* **Critical**: Fixed bug in ``differential_abundance.py`` fitZIG algorithm ([#1960](https://github.com/biocore/qiime/pull/1960)). **This was a serious bug that was encountered when users would call ``differential_abundance.py -a metagenomeSeq_fitZIG``. Any results previosuly generated with that command should be re-run.** +* **Critical**: Fixed bug in ``observation_metadata_correlation.py``, described in [#2009](https://github.com/biocore/qiime/issues/2009). **All previous output generated with ``observation_metadata_correlation.py`` was incorrect, and analyses using those results should be re-run.** This most commonly would have resulted in massive Type 2 error (false negatives), where observations whose abundance is correlated with metadata are not reported, though Type 1 error (false positives) are also possible. * ``count_seqs.py`` no longer fails on empty files. [#1991](https://github.com/biocore/qiime/issues/1991) * Updated minimum required version of [biom-format](http://github.com/biocore/biom-format) package to 2.1.4. This is a bug fix release. Details are available in the [biom-format ChangeLog](https://github.com/biocore/biom-format/blob/master/ChangeLog.md). * Updated minimum required version of [Emperor](http://github.com/biocore/emperor) package to 0.9.51. From 85ceed28b8a38fa0c96be6cce20e0cca97b58edf Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Tue, 26 May 2015 09:19:03 -0700 Subject: [PATCH 7/7] MAINT: set upper bound on natsort version the default sorting function changed in natsort 4.0. setting an upper bound on the required version to maintain the old default for consistency with prior versions of QIIME. See [biocore/scikit-bio#930](https://github.com/biocore/scikit-bio/issues/930) for more detail. --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index b4df58aae1..adff3d5b05 100644 --- a/setup.py +++ b/setup.py @@ -433,6 +433,7 @@ def build_swarm(): install_requires=['numpy >= 1.9.0', 'scipy >= 0.14.0', 'cogent == 1.5.3', + 'natsort < 4.0.0', 'matplotlib >= 1.1.0, != 1.4.2', 'pynast == 1.2.2', 'qcli >= 0.1.1, < 0.2.0', 'gdata', 'biom-format >= 2.1.4, < 2.2.0',