'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'
'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'
'/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
'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']
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'