comparison bwa_wrapper.py @ 2:3a001705dc94 draft default tip

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1:2ba834228e9b

    parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
    parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
    parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
    parser.add_option( '-I', '--illumina1.3', dest='illumina13qual', help='Input FASTQ files have Illuina 1.3 quality scores' )
    (options, args) = parser.parse_args()

    # output version # of tool
    try:
        tmp = tempfile.NamedTemporaryFile().name

        else:
            gen_alignment_cmds = ''
        if options.metadata_tsv:
	    f = open(options.metadata_tsv, 'r')
            cols = f.readline().split('\t')
            readGroup = '@RG\tID:1\tDS:%s\tPU:%s\tLB:%s\tCN:BMGC\tDT:%s\tFR:%s\tRR:%s\tPL:ILLUMINA' % ( cols[4], cols[16], cols[14], cols[1], cols[19], cols[20]  )
            gen_alignment_cmds += ' -r "%s"' % readGroup
            print readGroup
        if options.rgid:
            if not options.rglb or not options.rgpl or not options.rgsm:
                stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )

2:3a001705dc94

    parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
    parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
    parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
    parser.add_option( '-I', '--illumina1.3', dest='illumina13qual', help='Input FASTQ files have Illuina 1.3 quality scores' )
    parser.add_option( '', '--meta_tsv', dest='metadata_tsv', help='Meta data for filling things like sequencing center' )
    (options, args) = parser.parse_args()

    # output version # of tool
    try:
        tmp = tempfile.NamedTemporaryFile().name

        else:
            gen_alignment_cmds = ''
        if options.metadata_tsv:
	    f = open(options.metadata_tsv, 'r')
            cols = f.readline().split('\t')
            readGroup = '@RG\tID:%s\tDS:%s\tPU:%s\tLB:%s\tCN:BMGC\tDT:%s\tFR:%s\tRR:%s\tPL:ILLUMINA\tSM:%s' % ( cols[0], cols[4], cols[16], cols[14], cols[1], cols[19], cols[20], cols[18]  )
            gen_alignment_cmds += ' -r "%s"' % readGroup
            print readGroup
        if options.rgid:
            if not options.rglb or not options.rgpl or not options.rgsm:
                stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )