Mercurial > repos > yufei-luo > bwa_0_7_5
changeset 4:22449c3a0b7f draft default tip
debug when use 'history' input fasta as genome reference
| author | yufei-luo |
|---|---|
| date | Tue, 10 Dec 2013 08:48:23 -0500 |
| parents | 8409cff2d740 |
| children | |
| files | bwa_0_7_5/bwa_0_7_5.py |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/bwa_0_7_5/bwa_0_7_5.py Fri Nov 29 04:59:38 2013 -0500 +++ b/bwa_0_7_5/bwa_0_7_5.py Tue Dec 10 08:48:23 2013 -0500 @@ -66,7 +66,7 @@ parser.add_argument( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' ) parser.add_argument( '--rgid', help='Read group identifier' ) parser.add_argument( '--rgsm', help='Sample' ) - parser.add_argument( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT' and 'PACBIO' ], help='Platform/technology used to produce the reads' ) + parser.add_argument( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT', 'PACBIO' ], help='Platform/technology used to produce the reads' ) parser.add_argument( '--rglb', help='Library name' ) parser.add_argument( '--rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' ) parser.add_argument( '--rgcn', help='Sequencing center that produced the read' ) @@ -122,7 +122,8 @@ tmp_index_dir = tempfile.mkdtemp() tmp_dir = tempfile.mkdtemp() # index if necessary - if args.fileSource == 'history' and not args.do_not_build_index: + # if args.fileSource == 'history' and not args.do_not_build_index: + if args.fileSource == 'history' : ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close()