Пример #1
0
            'r1':
            '/home/cam/projects/forensics/forensics_data/MiSeq_DFSC/R701-A506_S5_L001_R1_001.fastq.gz',
            'single': 'single-end',
            'threads': '3',
        },
        'Trimmomatic': {
            'a': '',
            'd': False,
            'm': '20',
            'q': '20',
            's': True,
            'w': '4'
        },
        'strrazor': {
            'workdir': 'STRaitRazor',
            'opt': 'ALL',  # choice of X, Y, AUTOSOMAL, ALL
        },
    }

    if 1:
        interface['Shared']['single'] = 'auto-detect'

    if len(sys.argv) == 2:
        interface['Shared']['r1'] = sys.argv[1]

    success = strrazor(interface, progress=dummypb.StatusProgress())
    if success:
        print 'STRaitRazor pipeline completed successfully'
    else:
        print 'STRaitRazor pipeline failed'
Пример #2
0
        'Trimmomatic': {
            'c': False,
            # 'clip': 'ILLUMINACLIP:TruSeq3-SE:2:30:10',
            's': True,
            'w': '4',
            'q': '15',
            # 'minlen': 'MINLEN:30',
            'd': False,
            'm': '30',
            # 'phred': '-phred33',
        },
        'LobSTR': {
            'min-bp-before-indel': '7',
            'maximal-end-match': '15',
            'min-read-end-match': '5',
            'min-border': '5'
        }
    }
    import sys
    import dummypb
    if 0:
        interface['Shared']['single'] = 'auto-detect'
    if len(sys.argv) == 2:
        interface['Shared']['r1'] = sys.argv[1]

    success = lobstr(interface, progress=dummypb.StatusProgress())
    if success:
        print 'LobSTR pipeline completed successfully'
    else:
        print 'LobSTR pipeline failed'
Пример #3
0
            '/home/cam/projects/forensics/forensics_data/MiSeq_DFSC/R701-A506_S5_L001_R1_001.fastq.gz',
            'single': 'single-end',
            'threads': '2',
        },
        'Trimmomatic': {
            'clip': 'ILLUMINACLIP:TruSeq3-SE:2:30:10',
            'sliding': 'SLIDINGWINDOW:4:15',
            'w': '4',
            'q': '15',
            'minlen': 'MINLEN:30',
            'm': '30',
            'phred': '-phred33',
        }
    }
    if 0:
        interface['Shared']['single'] = 'paired-end'
    if 1:
        interface['Shared']['single'] = 'auto-detect'

    import dummypb
    if len(sys.argv) == 2:
        interface['Shared']['r1'] = sys.argv[1]

    res = prepare(interface, 'common', progress=dummypb.StatusProgress())

    print "prepare(...) returns:"
    print "   trim_fq =", res[0]
    print "   bn =", res[1]
    for cmd in res[2]:
        print "\t", cmd
Пример #4
0
            'phred': '-phred33',
        },
        'BWA': {
            'p': 'ILLUMINA',
            'T': '30'
        },
        'mpileup': {},
    }

    # parameters for paired end testing
    if 0:  # set paired end values
        interface['Shared'][
            'r1'] = '/home/cam/projects/forensics/forensics_data/MiSeq_DFSC/R701-A506_S5_L001_R1_001.fastq.gz'
        interface['Shared']['single'] = 'single-end'

    if 0:  # run deduplication step
        interface['Shared']['dedup'] = True

    if 1:
        interface['Shared']['single'] = 'auto-detect'

    if len(sys.argv) == 2:
        interface['Shared']['r1'] = sys.argv[1]

    success = tovcf(interface, progress=dummypb.StatusProgress())
    if success:
        print 'ToVCF pipeline completed successfully'
    else:
        print 'ToVCF pipeline failed'
    print "... using", interface['Shared']['tovcf']
Пример #5
0
    progress.status('Step 1 - extracting FASTQ file(s)')
    files, sf = com.bam2fq(srcdir, dstdir, args['single'])
    cmds = [(None, 'b')]  # first task shows up on progress bar
    for f in files:
        # use -f flag to avoid user dialog - force progress/overwrite
        cmds.append(([loc['gzip'], '-f', f], 'nb'))

    success = px.run_pipeline(cmds, logger=logger, progress=progress)
    if success:
        progress.status('conversion complete')

    return success


if __name__ == '__main__':
    """ run the BAM to FASTQ process"""
    import sys
    import dummypb as sp

    # define dummy interface output so we can get started
    interface = {'Shared': {}, 'BAMtoFQ': {}}
    assert len(sys.argv) == 2

    interface['BAMtoFQ']['b'] = sys.argv[1]
    success = bamToFQ(interface, progress=sp.StatusProgress())

    if success:
        print 'BAM converted to FASTQ successfully'
    else:
        print 'BAM conversion to FASTQ failure'