From 40f31e137f097a13d948edbcd95e76190d6a9584 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Wed, 11 May 2016 15:23:34 +0000 Subject: [PATCH 1/3] Add warnings for the --reference option --- scripts/iva | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) mode change 100644 => 100755 scripts/iva diff --git a/scripts/iva b/scripts/iva old mode 100644 new mode 100755 index 55dd7e2..7ae78c0 --- a/scripts/iva +++ b/scripts/iva @@ -34,7 +34,7 @@ io_group.add_argument('-r', '--reads_rev', action=iva.common.abspathAction, help io_group.add_argument('--fr', action=iva.common.abspathAction, dest='reads', help='Name of interleaved fasta/q file', metavar='filename[.gz]') io_group.add_argument('--keep_files', action='store_true', help='Keep intermediate files (could be many!). Default is to delete all unnecessary files') io_group.add_argument('--contigs', action=iva.common.abspathAction, help='Fasta file of contigs to be extended. Incompatible with --reference', metavar='filename[.gz]') -io_group.add_argument('--reference', action=iva.common.abspathAction, help='Fasta file of reference genome, or parts thereof. IVA will try to assemble one contig per sequence in this file. Incompatible with --contigs', metavar='filename[.gz]') +io_group.add_argument('--reference', action=iva.common.abspathAction, help='EXPERIMENTAL! This option is EXPERIMENTAL, not recommended, and has not been tested! Fasta file of reference genome, or parts thereof. IVA will try to assemble one contig per sequence in this file. Incompatible with --contigs', metavar='filename[.gz]') io_group.add_argument('-v', '--verbose', action='count', help='Be verbose by printing messages to stdout. Use up to three times for increasing verbosity.', default=0) @@ -112,6 +112,9 @@ if options.contigs and options.reference: print('Error! Cannot use both of --contgs and --reference. Cannot continue', file=sys.stderr) sys.exit(1) +if options.reference: + print('WARNING. The option --reference has been used. It is EXPERIMENTAL and it is probably better to not use it!', file=sys.stderr) + if os.path.exists(options.outdir): print('Error! Output directory', options.outdir, 'already exists. Cannot continue', file=sys.stderr) sys.exit(1) @@ -209,6 +212,8 @@ if options.contigs: contigs = 'contigs_to_extend.fasta' pyfastaq.tasks.to_fasta(options.contigs, contigs, line_length=60, strip_after_first_whitespace=True) elif options.reference: + print('WARNING. The option --reference has been used. Trying to use reference file to generate starting contig.', file=sys.stderr) + print(' ... if this throws errors, then try running without the --reference option', file=sys.stderr) reference = 'reference_in.fasta' pyfastaq.tasks.to_fasta(options.reference, reference, line_length=60, strip_after_first_whitespace=True) p = iva.seed_processor.SeedProcessor( From 8af7ca616f1b2d3b85c774392c54c08cd6ac9b9e Mon Sep 17 00:00:00 2001 From: martinghunt Date: Wed, 11 May 2016 15:24:03 +0000 Subject: [PATCH 2/3] make executable --- scripts/iva_qc | 0 scripts/iva_qc_make_db | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 scripts/iva_qc mode change 100644 => 100755 scripts/iva_qc_make_db diff --git a/scripts/iva_qc b/scripts/iva_qc old mode 100644 new mode 100755 diff --git a/scripts/iva_qc_make_db b/scripts/iva_qc_make_db old mode 100644 new mode 100755 From 13d5d2183c5465574b3652f193441c5a5da51812 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Wed, 11 May 2016 15:25:18 +0000 Subject: [PATCH 3/3] Version bump 1.0.6 --- iva/common.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/iva/common.py b/iva/common.py index dfaed4d..b7d7418 100644 --- a/iva/common.py +++ b/iva/common.py @@ -16,7 +16,7 @@ import os import sys import subprocess -version = '1.0.5' +version = '1.0.6' class abspathAction(argparse.Action): def __call__(self, parser, namespace, value, option_string): diff --git a/setup.py b/setup.py index f6b1f93..cdd1d09 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ setup( name='iva', - version='1.0.5', + version='1.0.6', description='Iterative Virus Assembler', packages = find_packages(), package_data={'iva': ['gage/*', 'ratt/*', 'read_trim/*', 'test_run_data/*']},