comparison shear_wrapper.py @ 6:0158f7356ffd

Add new outputs and params to shear_sv.xml for version 2.3

5:aaaa5a071ff0

    parser.add_option( '-B', '--bai', dest='bai', help='BAM index file (.bai)' )
    parser.add_option( '-f', '--fasta_reference', dest='fasta', help='The reference sequence fasta file' )
    parser.add_option( '-F', '--fasta_index', dest='fai', help='The .fai index file for the reference sequence fasta' )
    parser.add_option( '-t', '--twobit', dest='twobit', help='The .2bit encoding of the reference sequence fasta generated by faToTwoBit' )
    parser.add_option( '-i', '--bwa_index', dest='bwa_index', help='The bwa index of the reference sequence' )
    parser.add_option( '-r', '--report', dest='report', help='The SHEAR output report' )
    parser.add_option( '-s', '--sdi', dest='sdi', help='The SHEAR sdi input from the SHEAR sv command' )
    parser.add_option( '-o', '--output', dest='output', help='The SHEAR output assembly fasta file' )
    parser.add_option( '-D', '--svidx_dir', dest='svidx_dir', help='The SHEAR output assembly fasta file' )
    (options, args) = parser.parse_args()

    def make_ref(src, dest, copy=False):
        if copy:
            shutil.copy( src, dest )

    copy_ref = False
    prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref'
    if command in ['sv']:
        args.append( '-p' )
        args.append( prefix )
    if options.svidx_dir and command in ['sv']:
        if not os.path.isdir(options.svidx_dir):
            os.makedirs(options.svidx_dir)
        ref_prefix = os.path.join(options.svidx_dir,prefix)
        copy_ref = True

    try:
        proc = subprocess.Popen( args=args, shell=False )
        returncode = proc.wait()
        if returncode != 0:
            stop_err( 'Error running SHEAR ' + command, returncode )
        if command in ['sv']:
            report_path = os.path.join(os.getcwd(),prefix + '.report')
            if os.path.exists(report_path):
                if options.report:
                    shutil.copy(report_path,options.report)
            else:
                raise Exception, 'no report file'
            sdi_path = os.path.join(os.getcwd(),prefix + '.sdi')
            if os.path.exists(sdi_path):
                if options.sdi:
                    shutil.copy(sdi_path,options.sdi)
            else:
                raise Exception, 'no sdi file'
    except Exception, e:
        # clean up temp dirs
        stop_err( 'Error running SHEAR %s %s' % (command,str(e)),9 )

if __name__=="__main__": __main__()

6:0158f7356ffd

    parser.add_option( '-B', '--bai', dest='bai', help='BAM index file (.bai)' )
    parser.add_option( '-f', '--fasta_reference', dest='fasta', help='The reference sequence fasta file' )
    parser.add_option( '-F', '--fasta_index', dest='fai', help='The .fai index file for the reference sequence fasta' )
    parser.add_option( '-t', '--twobit', dest='twobit', help='The .2bit encoding of the reference sequence fasta generated by faToTwoBit' )
    parser.add_option( '-i', '--bwa_index', dest='bwa_index', help='The bwa index of the reference sequence' )
    parser.add_option( '-R', '--report', dest='report', help='The SHEAR output report' )
    parser.add_option( '-s', '--sdi', dest='sdi', help='The SHEAR sdi input from the SHEAR sv command' )
    parser.add_option( '-o', '--output', dest='output', help='The SHEAR output assembly fasta file' )
    parser.add_option( '-D', '--svidx_dir', dest='svidx_dir', help='The SHEAR output assembly fasta file' )
    parser.add_option( '-S', '--sv-only', dest='sv_only', action="store_true", help='SV Only prediction mode.' )
    parser.add_option( '-r', '--region', dest='region', help='Region of the input alignment to analyze' )
    (options, args) = parser.parse_args()

    def make_ref(src, dest, copy=False):
        if copy:
            shutil.copy( src, dest )

    copy_ref = False
    prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref'
    if command in ['sv']:
        args.append( '-p' )
        args.append( prefix )
        if options.sv_only:
            args.append('--sv-only')
        if options.region:
            args.append('-r')
            args.append(options.region)
    if options.svidx_dir and command in ['sv']:
        if not os.path.isdir(options.svidx_dir):
            os.makedirs(options.svidx_dir)
        ref_prefix = os.path.join(options.svidx_dir,prefix)
        copy_ref = True

    try:
        proc = subprocess.Popen( args=args, shell=False )
        returncode = proc.wait()
        if returncode != 0:
            stop_err( 'Error running SHEAR ' + command, returncode )
    except Exception, e:
        # clean up temp dirs
        stop_err( 'Error running SHEAR %s %s' % (command,str(e)),9 )

if __name__=="__main__": __main__()