Merge branch 'development'

ratschlab · Nov 18, 2019 · 324d45c · 324d45c
2 parents a7009fb + fcc4b40
commit 324d45c
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Showing 49 changed files with 1 addition and 1 deletion.
diff --git a/spladder/helpers.py b/spladder/helpers.py
@@ -100,7 +100,7 @@ def get_filename(which, options, sample_idx=None):
     if which in ['fn_count_in', 'fn_count_out']:
         if options.spladderfile == '-':
             if options.merge == 'single':
-                fname = os.path.join(options.outdir, 'spladder', 'genes_graph_conf%i.single.%s%s.pickle' % (options.confidence, options.samples[sample_idx], prune_tag))
+                fname = os.path.join(options.outdir, 'spladder', 'genes_graph_conf%i.%s%s.pickle' % (options.confidence, options.samples[sample_idx], prune_tag))
             else:
                 if (options.qmode == 'single' and which != 'fn_count_in') or (options.qmode == 'collect' and which == 'fn_count_in'):
                     fname = os.path.join(options.outdir, 'spladder', 'genes_graph_conf%i.%s.%s%s%s.pickle' % (options.confidence, options.merge, options.samples[sample_idx], prune_tag, validate_tag))

diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mult_exon_skip_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_mult_exon_skip_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/spladder/genes_graph_conf3.merge_graphs.count.hdf5 b/tests/testcase_events/results_merged/spladder/genes_graph_conf3.merge_graphs.count.hdf5
diff --git a/tests/testcase_events/results_merged/spladder/genes_graph_conf3.merge_graphs.gene_exp.hdf5 b/tests/testcase_events/results_merged/spladder/genes_graph_conf3.merge_graphs.gene_exp.hdf5
diff --git a/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.log10.ps b/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.log10.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.ps b/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/dispersion_adjusted_exon_skip.ps b/tests/testcase_events/results_merged/testing/plots/dispersion_adjusted_exon_skip.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/dispersion_fitted_exon_skip.ps b/tests/testcase_events/results_merged/testing/plots/dispersion_fitted_exon_skip.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/dispersion_raw_exon_skip.ps b/tests/testcase_events/results_merged/testing/plots/dispersion_raw_exon_skip.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/ma_plot_exon_skip.ps b/tests/testcase_events/results_merged/testing/plots/ma_plot_exon_skip.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.log10.ps b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.log10.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.ps b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.log10.ps b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.log10.ps
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.ps b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.ps