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comparison bwa_0_7_5/bwa_0_7_5.py @ 4:22449c3a0b7f draft default tip

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debug when use 'history' input fasta as genome reference
author yufei-luo
date Tue, 10 Dec 2013 08:48:23 -0500
parents 8409cff2d740
children
comparison
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3:8409cff2d740 4:22449c3a0b7f
64 parser.add_argument( '-L', '--clipping', default=5, type=int, help='penalty for clipping [5]' ) 64 parser.add_argument( '-L', '--clipping', default=5, type=int, help='penalty for clipping [5]' )
65 parser.add_argument( '-U', '--unpairedReadpair', default=17, type=int, help='penalty for an unpaired read pair [17]' ) 65 parser.add_argument( '-U', '--unpairedReadpair', default=17, type=int, help='penalty for an unpaired read pair [17]' )
66 parser.add_argument( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' ) 66 parser.add_argument( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' )
67 parser.add_argument( '--rgid', help='Read group identifier' ) 67 parser.add_argument( '--rgid', help='Read group identifier' )
68 parser.add_argument( '--rgsm', help='Sample' ) 68 parser.add_argument( '--rgsm', help='Sample' )
69 parser.add_argument( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT' and 'PACBIO' ], help='Platform/technology used to produce the reads' ) 69 parser.add_argument( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT', 'PACBIO' ], help='Platform/technology used to produce the reads' )
70 parser.add_argument( '--rglb', help='Library name' ) 70 parser.add_argument( '--rglb', help='Library name' )
71 parser.add_argument( '--rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' ) 71 parser.add_argument( '--rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' )
72 parser.add_argument( '--rgcn', help='Sequencing center that produced the read' ) 72 parser.add_argument( '--rgcn', help='Sequencing center that produced the read' )
73 parser.add_argument( '--rgds', help='Description' ) 73 parser.add_argument( '--rgds', help='Description' )
74 parser.add_argument( '--rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' ) 74 parser.add_argument( '--rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' )
120 120
121 # make temp directory for placement of indices 121 # make temp directory for placement of indices
122 tmp_index_dir = tempfile.mkdtemp() 122 tmp_index_dir = tempfile.mkdtemp()
123 tmp_dir = tempfile.mkdtemp() 123 tmp_dir = tempfile.mkdtemp()
124 # index if necessary 124 # index if necessary
125 if args.fileSource == 'history' and not args.do_not_build_index: 125 # if args.fileSource == 'history' and not args.do_not_build_index:
126 if args.fileSource == 'history' :
126 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) 127 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
127 ref_file_name = ref_file.name 128 ref_file_name = ref_file.name
128 ref_file.close() 129 ref_file.close()
129 os.symlink( args.ref, ref_file_name ) 130 os.symlink( args.ref, ref_file_name )
130 # determine which indexing algorithm to use, based on size 131 # determine which indexing algorithm to use, based on size