def __main__():
logging.basicConfig(level=logging.INFO)
time.sleep(1) #small hack, sometimes it seems like docker file systems aren't avalible instantly
parser = argparse.ArgumentParser(description='')
parser.add_argument('-r', dest='inputFastaFile', required=True, help='the reference file')
parser.add_argument('-R', dest='inputFastaName', default="genome", help='the reference name')
parser.add_argument('-b', dest='inputBamFiles', default=[], action="append", help='the bam file')
parser.add_argument('-bi', dest='inputBamFileIndexes', default=[], action="append", help='the bam file')
parser.add_argument('-s', dest='insert_sizes', type=int, default=[], action="append", required=False, help='the insert size')
parser.add_argument('-t', dest='sampleTags', default=[], action="append", help='the sample tag')
parser.add_argument('-o1', dest='outputRaw', help='the output raw', default=None)
parser.add_argument('-o2', dest='outputVcfFile', help='the output vcf', default=None)
parser.add_argument('-o3', dest='outputSomaticVcfFile', help='the output somatic filtered vcf', default=None)
parser.add_argument('--number_of_threads', dest='number_of_threads', type=int, default=2)
parser.add_argument('--number_of_procs', dest='procs', type=int, default=1)
parser.add_argument('--breakdancer', dest='breakdancer')
parser.add_argument('-x', '--max_range_index', dest='max_range_index', type=int, default=None)
parser.add_argument('--window_size', dest='window_size', type=int, default=None)
parser.add_argument('--sequencing_error_rate', dest='sequencing_error_rate', type=float, default=None)
parser.add_argument('--sensitivity', dest='sensitivity', default=None, type=float)
parser.add_argument('--report_long_insertions', dest='report_long_insertions', action='store_true', default=False)
parser.add_argument('--report_duplications', dest='report_duplications', action='store_true', default=False)
parser.add_argument('--report_inversions', dest='report_inversions', action='store_true', default=False)
parser.add_argument('--report_breakpoints', dest='report_breakpoints', action='store_true', default=False)
parser.add_argument('-u', '--maximum_allowed_mismatch_rate', dest='maximum_allowed_mismatch_rate', type=float, default=None)
parser.add_argument('--report_close_mapped_reads', dest='report_close_mapped_reads', action='store_true', default=False)
parser.add_argument('--report_only_close_mapped_reads', dest='report_only_close_mapped_reads', action='store_true', default=False)
parser.add_argument('--report_interchromosomal_events', dest='report_interchromosomal_events', action='store_true', default=False)
parser.add_argument('--IndelCorrection', dest='IndelCorrection', action='store_true', default=False)
parser.add_argument('--NormalSamples', dest='NormalSamples', action='store_true', default=False)
parser.add_argument('-a', '--additional_mismatch', dest='additional_mismatch', type=int, default=None)
parser.add_argument('-m', '--min_perfect_match_around_BP', dest='min_perfect_match_around_BP', type=int, default=None)
parser.add_argument('-v', '--min_inversion_size', dest='min_inversion_size', type=int, default=None)
parser.add_argument('-d', '--min_num_matched_bases', dest='min_num_matched_bases', type=int, default=None)
parser.add_argument('-B', '--balance_cutoff', dest='balance_cutoff', type=int, default=None)
parser.add_argument('-A', '--anchor_quality', dest='anchor_quality', type=int, default=None)
parser.add_argument('-M', '--minimum_support_for_event', dest='minimum_support_for_event', type=int, default=None)
parser.add_argument('-n', '--NM', dest='NM', type=int, default=None)
parser.add_argument('--detect_DD', dest='detect_DD', action='store_true', default=False)
parser.add_argument('--MAX_DD_BREAKPOINT_DISTANCE', dest='MAX_DD_BREAKPOINT_DISTANCE', type=int, default='350')
parser.add_argument('--MAX_DISTANCE_CLUSTER_READS', dest='MAX_DISTANCE_CLUSTER_READS', type=int, default='100')
parser.add_argument('--MIN_DD_CLUSTER_SIZE', dest='MIN_DD_CLUSTER_SIZE', type=int, default='3')
parser.add_argument('--MIN_DD_BREAKPOINT_SUPPORT', dest='MIN_DD_BREAKPOINT_SUPPORT', type=int, default='3')
parser.add_argument('--MIN_DD_MAP_DISTANCE', dest='MIN_DD_MAP_DISTANCE', type=int, default='8000')
parser.add_argument('--DD_REPORT_DUPLICATION_READS', dest='DD_REPORT_DUPLICATION_READS', action='store_true', default=False)
parser.add_argument('--somatic_vaf', type=float, default=0.08)
parser.add_argument('--somatic_cov', type=int, default=20)
parser.add_argument('--somatic_hom', type=int, default=6)
parser.add_argument("-J", "--exclude", dest="exclude", default=None)
parser.add_argument("-j", "--include", dest="include", default=None)
parser.add_argument('--min_chrom_size', dest='min_chrom_size', type=int, default='1')
parser.add_argument('-z', '--input_SV_Calls_for_assembly', dest='input_SV_Calls_for_assembly', action='store_true', default=False)
parser.add_argument('--workdir', default="./")
parser.add_argument('--no_clean', action="store_true", default=False)
args = parser.parse_args()
inputBamFiles = list( os.path.abspath(a) for a in args.inputBamFiles )
if len(inputBamFiles) == 0:
logging.error("Need input files")
sys.exit(1)
inputBamFileIndexes = list( os.path.abspath(a) for a in args.inputBamFileIndexes )
if len(inputBamFileIndexes) == 0:
inputBamFileIndexes = [None] * len(inputBamFiles)
if len(inputBamFileIndexes) != len(inputBamFiles):
logging.error("Index file count needs to undefined or match input file count")
sys.exit(1)
insertSizes = args.insert_sizes
if len(insertSizes) == 0:
insertSizes = [None] * len(inputBamFiles)
if len(insertSizes) != len(inputBamFiles):
logging.error("Insert Sizes needs to undefined or match input file count")
sys.exit(1)
sampleTags = args.sampleTags
if len(sampleTags) != len(inputBamFiles):
logging.error("Sample Tags need to match input file count")
sys.exit(1)
tempDir = tempfile.mkdtemp(dir=args.workdir, prefix="pindel_work_")
print(tempDir)
try:
meanInsertSizes = []
seq_hash = {}
newInputFiles = []
i = 0
#make sure the BAMs are indexed and get the mean insert sizes
for inputBamFile, inputBamIndex, insertSize, sampleTag in zip(inputBamFiles, inputBamFileIndexes, insertSizes, sampleTags ):
inputFastaFile, inputBamFile = indexBam(args.workdir, args.inputFastaFile, inputBamFile, i, inputBamIndex)
i += 1
newInputFiles.append(inputBamFile)
if insertSize==None:
meanInsertSize = getMeanInsertSize(inputBamFile)
else:
meanInsertSize=insertSize
meanInsertSizes.append( meanInsertSize )
for seq in get_bam_seq(inputBamFile, args.min_chrom_size):
seq_hash[seq] = True
seqs = seq_hash.keys()
configFile = config(newInputFiles, meanInsertSizes, sampleTags, tempDir)
#run pindel
pindel_files = []
if args.procs == 1:
cmd, pindelFileBase = pindel(inputFastaFile, configFile, args, tempDir)
execute(cmd)
for suffix in ["_D", "_SI", "_LI", "_INV", "_TD"]:
if os.path.exists(pindelFileBase + suffix):
pindel_files.append( pindelFileBase + suffix )
else:
cmds = []
runs = []
for a in seqs:
cmd, pindelFileBase = pindel(inputFastaFile, configFile, args, tempDir, a)
cmds.append(cmd)
runs.append(pindelFileBase)
p = Pool(args.procs)
values = p.map(execute, cmds, 1)
for pindelFileBase in runs:
for suffix in ["_D", "_SI", "_LI", "_INV", "_TD"]:
if os.path.exists(pindelFileBase + suffix):
pindel_files.append( pindelFileBase + suffix )
#run pindel2vcf
with open(os.path.join(args.workdir, "pindel_all"), "w") as handle:
for p in pindel_files:
with open(p) as ihandle:
for line in ihandle:
handle.write(line)
if args.outputRaw is not None:
shutil.copy(os.path.join(args.workdir, "pindel_all"), args.outputRaw)
if args.outputVcfFile is not None:
cmd = pindel2vcf(inputFastaFile, args.inputFastaName, os.path.join(args.workdir, "pindel_all"), args.outputVcfFile)
execute(cmd)
if args.outputSomaticVcfFile is not None:
with open(os.path.join(args.workdir, "pindel_somatic"), "w") as handle:
for p in pindel_files:
if p.endswith("_D"):
with open(p) as ihandle:
for line in ihandle:
if re.search("ChrID", line):
handle.write(line)
for p in pindel_files:
if p.endswith("_SI"):
with open(p) as ihandle:
for line in ihandle:
if re.search("ChrID", line):
handle.write(line)
with open(os.path.join(args.workdir, "somatic.indel.filter.config"), "w") as handle:
handle.write("indel.filter.input = %s\n" % os.path.join(args.workdir, "pindel_somatic"))
handle.write("indel.filter.vaf = %s\n" % (args.somatic_vaf))
handle.write("indel.filter.cov = %s\n" % (args.somatic_cov))
handle.write("indel.filter.hom = %s\n" % (args.somatic_hom))
handle.write("indel.filter.pindel2vcf = %s\n" % (which("pindel2vcf")))
handle.write("indel.filter.reference = %s\n" % (inputFastaFile))
handle.write("indel.filter.referencename = %s\n" % (args.inputFastaName))
handle.write("indel.filter.referencedate = %s\n" % (datetime.datetime.now().strftime("%Y%m%d")) )
handle.write("indel.filter.output = %s\n" % (args.outputSomaticVcfFile))
# The hard-coded paths need to be removed.
execute("%s ~/bin/somatic_indelfilter.pl %s" % (which("perl"), os.path.join(args.workdir, "somatic.indel.filter.config")) )
finally:
if not args.no_clean and os.path.exists(tempDir):
shutil.rmtree(tempDir)
def __main__():
logging.basicConfig(level=logging.INFO)
time.sleep(
1
) #small hack, sometimes it seems like docker file systems aren't avalible instantly
parser = argparse.ArgumentParser(description='')
parser.add_argument('-r',
dest='inputFastaFile',
required=True,
help='the reference file')
parser.add_argument('-R',
dest='inputFastaName',
default="genome",
help='the reference name')
parser.add_argument('-b',
dest='inputBamFiles',
default=[],
action="append",
help='the bam file')
parser.add_argument('-bi',
dest='inputBamFileIndexes',
default=[],
action="append",
help='the bam file')
parser.add_argument('-s',
dest='insert_sizes',
type=int,
default=[],
action="append",
required=False,
help='the insert size')
parser.add_argument('-t',
dest='sampleTags',
default=[],
action="append",
help='the sample tag')
parser.add_argument('-o1',
dest='outputRaw',
help='the output raw',
default=None)
parser.add_argument('-o2',
dest='outputVcfFile',
help='the output vcf',
default=None)
parser.add_argument('-o3',
dest='outputSomaticVcfFile',
help='the output somatic filtered vcf',
default=None)
parser.add_argument('--number_of_threads',
dest='number_of_threads',
type=int,
default=2)
parser.add_argument('--number_of_procs', dest='procs', type=int, default=1)
parser.add_argument('--breakdancer', dest='breakdancer')
parser.add_argument('-x',
'--max_range_index',
dest='max_range_index',
type=int,
default=None)
parser.add_argument('--window_size',
dest='window_size',
type=int,
default=None)
parser.add_argument('--sequencing_error_rate',
dest='sequencing_error_rate',
type=float,
default=None)
parser.add_argument('--sensitivity',
dest='sensitivity',
default=None,
type=float)
parser.add_argument('--report_long_insertions',
dest='report_long_insertions',
action='store_true',
default=False)
parser.add_argument('--report_duplications',
dest='report_duplications',
action='store_true',
default=False)
parser.add_argument('--report_inversions',
dest='report_inversions',
action='store_true',
default=False)
parser.add_argument('--report_breakpoints',
dest='report_breakpoints',
action='store_true',
default=False)
parser.add_argument('-u',
'--maximum_allowed_mismatch_rate',
dest='maximum_allowed_mismatch_rate',
type=float,
default=None)
parser.add_argument('--report_close_mapped_reads',
dest='report_close_mapped_reads',
action='store_true',
default=False)
parser.add_argument('--report_only_close_mapped_reads',
dest='report_only_close_mapped_reads',
action='store_true',
default=False)
parser.add_argument('--report_interchromosomal_events',
dest='report_interchromosomal_events',
action='store_true',
default=False)
parser.add_argument('--IndelCorrection',
dest='IndelCorrection',
action='store_true',
default=False)
parser.add_argument('--NormalSamples',
dest='NormalSamples',
action='store_true',
default=False)
parser.add_argument('-a',
'--additional_mismatch',
dest='additional_mismatch',
type=int,
default=None)
parser.add_argument('-m',
'--min_perfect_match_around_BP',
dest='min_perfect_match_around_BP',
type=int,
default=None)
parser.add_argument('-v',
'--min_inversion_size',
dest='min_inversion_size',
type=int,
default=None)
parser.add_argument('-d',
'--min_num_matched_bases',
dest='min_num_matched_bases',
type=int,
default=None)
parser.add_argument('-B',
'--balance_cutoff',
dest='balance_cutoff',
type=int,
default=None)
parser.add_argument('-A',
'--anchor_quality',
dest='anchor_quality',
type=int,
default=None)
parser.add_argument('-M',
'--minimum_support_for_event',
dest='minimum_support_for_event',
type=int,
default=None)
parser.add_argument('-n', '--NM', dest='NM', type=int, default=None)
parser.add_argument('--detect_DD',
dest='detect_DD',
action='store_true',
default=False)
parser.add_argument('--MAX_DD_BREAKPOINT_DISTANCE',
dest='MAX_DD_BREAKPOINT_DISTANCE',
type=int,
default='350')
parser.add_argument('--MAX_DISTANCE_CLUSTER_READS',
dest='MAX_DISTANCE_CLUSTER_READS',
type=int,
default='100')
parser.add_argument('--MIN_DD_CLUSTER_SIZE',
dest='MIN_DD_CLUSTER_SIZE',
type=int,
default='3')
parser.add_argument('--MIN_DD_BREAKPOINT_SUPPORT',
dest='MIN_DD_BREAKPOINT_SUPPORT',
type=int,
default='3')
parser.add_argument('--MIN_DD_MAP_DISTANCE',
dest='MIN_DD_MAP_DISTANCE',
type=int,
default='8000')
parser.add_argument('--DD_REPORT_DUPLICATION_READS',
dest='DD_REPORT_DUPLICATION_READS',
action='store_true',
default=False)
parser.add_argument('--somatic_vaf', type=float, default=0.08)
parser.add_argument('--somatic_cov', type=int, default=20)
parser.add_argument('--somatic_hom', type=int, default=6)
parser.add_argument("-J", "--exclude", dest="exclude", default=None)
parser.add_argument("-j", "--include", dest="include", default=None)
parser.add_argument('--min_chrom_size',
dest='min_chrom_size',
type=int,
default='1')
parser.add_argument('-z',
'--input_SV_Calls_for_assembly',
dest='input_SV_Calls_for_assembly',
action='store_true',
default=False)
parser.add_argument('--workdir', default="./")
parser.add_argument('--no_clean', action="store_true", default=False)
args = parser.parse_args()
inputBamFiles = list(os.path.abspath(a) for a in args.inputBamFiles)
if len(inputBamFiles) == 0:
logging.error("Need input files")
sys.exit(1)
inputBamFileIndexes = list(
os.path.abspath(a) for a in args.inputBamFileIndexes)
if len(inputBamFileIndexes) == 0:
inputBamFileIndexes = [None] * len(inputBamFiles)
if len(inputBamFileIndexes) != len(inputBamFiles):
logging.error(
"Index file count needs to undefined or match input file count")
sys.exit(1)
insertSizes = args.insert_sizes
if len(insertSizes) == 0:
insertSizes = [None] * len(inputBamFiles)
if len(insertSizes) != len(inputBamFiles):
logging.error(
"Insert Sizes needs to undefined or match input file count")
sys.exit(1)
sampleTags = args.sampleTags
if len(sampleTags) != len(inputBamFiles):
logging.error("Sample Tags need to match input file count")
sys.exit(1)
tempDir = tempfile.mkdtemp(dir=args.workdir, prefix="pindel_work_")
print(tempDir)
try:
meanInsertSizes = []
seq_hash = {}
newInputFiles = []
i = 0
#make sure the BAMs are indexed and get the mean insert sizes
for inputBamFile, inputBamIndex, insertSize, sampleTag in zip(
inputBamFiles, inputBamFileIndexes, insertSizes, sampleTags):
inputFastaFile, inputBamFile = indexBam(args.workdir,
args.inputFastaFile,
inputBamFile, i,
inputBamIndex)
i += 1
newInputFiles.append(inputBamFile)
if insertSize == None:
meanInsertSize = getMeanInsertSize(inputBamFile)
else:
meanInsertSize = insertSize
meanInsertSizes.append(meanInsertSize)
for seq in get_bam_seq(inputBamFile, args.min_chrom_size):
seq_hash[seq] = True
seqs = seq_hash.keys()
configFile = config(newInputFiles, meanInsertSizes, sampleTags,
tempDir)
#run pindel
pindel_files = []
if args.procs == 1:
cmd, pindelFileBase = pindel(inputFastaFile, configFile, args,
tempDir)
execute(cmd)
for suffix in ["_D", "_SI", "_LI", "_INV", "_TD"]:
if os.path.exists(pindelFileBase + suffix):
pindel_files.append(pindelFileBase + suffix)
else:
cmds = []
runs = []
for a in seqs:
cmd, pindelFileBase = pindel(inputFastaFile, configFile, args,
tempDir, a)
cmds.append(cmd)
runs.append(pindelFileBase)
p = Pool(args.procs)
values = p.map(execute, cmds, 1)
for pindelFileBase in runs:
for suffix in ["_D", "_SI", "_LI", "_INV", "_TD"]:
if os.path.exists(pindelFileBase + suffix):
pindel_files.append(pindelFileBase + suffix)
#run pindel2vcf
with open(os.path.join(args.workdir, "pindel_all"), "w") as handle:
for p in pindel_files:
with open(p) as ihandle:
for line in ihandle:
handle.write(line)
if args.outputRaw is not None:
shutil.copy(os.path.join(args.workdir, "pindel_all"),
args.outputRaw)
if args.outputVcfFile is not None:
cmd = pindel2vcf(inputFastaFile, args.inputFastaName,
os.path.join(args.workdir, "pindel_all"),
args.outputVcfFile)
execute(cmd)
if args.outputSomaticVcfFile is not None:
with open(os.path.join(args.workdir, "pindel_somatic"),
"w") as handle:
for p in pindel_files:
if p.endswith("_D"):
with open(p) as ihandle:
for line in ihandle:
if re.search("ChrID", line):
handle.write(line)
for p in pindel_files:
if p.endswith("_SI"):
with open(p) as ihandle:
for line in ihandle:
if re.search("ChrID", line):
handle.write(line)
with open(
os.path.join(args.workdir, "somatic.indel.filter.config"),
"w") as handle:
handle.write("indel.filter.input = %s\n" %
os.path.join(args.workdir, "pindel_somatic"))
handle.write("indel.filter.vaf = %s\n" % (args.somatic_vaf))
handle.write("indel.filter.cov = %s\n" % (args.somatic_cov))
handle.write("indel.filter.hom = %s\n" % (args.somatic_hom))
handle.write("indel.filter.pindel2vcf = %s\n" %
(which("pindel2vcf")))
handle.write("indel.filter.reference = %s\n" %
(inputFastaFile))
handle.write("indel.filter.referencename = %s\n" %
(args.inputFastaName))
handle.write("indel.filter.referencedate = %s\n" %
(datetime.datetime.now().strftime("%Y%m%d")))
handle.write("indel.filter.output = %s\n" %
(args.outputSomaticVcfFile))
execute(
"%s /home/exacloud/clinical/RichardsLab/bin/somatic_indelfilter.pl %s"
% (which("perl"),
os.path.join(args.workdir, "somatic.indel.filter.config")))
finally:
if not args.no_clean and os.path.exists(tempDir):
shutil.rmtree(tempDir)
