def map(self):
sf = pysam.Samfile(self.input)
rgs = [i['ID'] for i in sf.header["RG"]]
sf.close()
self.newsams = [
os.path.join(os.getcwd(), str(uuid.uuid4())) + ".sam"
for i in range(len(rgs))
]
for readgroup, samout in zip(rgs, self.newsams):
append = "--substitutionrate={0} -g {1} -h {1} -M {2} -o {3} --logfile={3}.log --readgroup=ID:{4} --outputformat=sam -v 3 ".format(
self.subrate, self.ref, self.input, samout, readgroup)
if self.keepgoodreads: stampyCmd += " --bamkeepgoodreads "
if self.alignquals: stampyCmd += " --alignquals "
if self.baq: stampyCmd += " --baq "
cmd, stdout, stderr, errcode = COMPASSCFG["tools"][
"stampy"].execute(append=append)
cmd, stdout, stderr, errcode = "", "", "", 0
LE.debug(StringIO(stdout), "stdout")
LE.debug(StringIO(stderr), "stderr")
if errcode:
LE.critical("Stampy execution failed {0}".format(errcode))
raise Exception("Stampy execution failed {0}".format(errcode))
self.insertsizes[readgroup] = self.generateSeqStats(samout)
def markDuplicates(self):
cmd, stdout, stderr, errcode = COMPASSCFG['tools']['picard'].execute(
source='path',
file='MarkDuplicates.jar',
prepend='java -jar',
append=
"I={0} O={0}.dedup METRICS_FILE={1}_metrics.txt ASSUME_SORTED=true VERBOSITY=DEBUG VALIDATION_STRINGENCY=SILENT"
.format(self.output, self.input))
LE.debug(StringIO(stdout), "stdout")
LE.debug(StringIO(stderr), "stderr")
if errcode:
LE.critical("MarkDuplicates execution failed {0}".format(errcode))
raise Exception(
"MarkDuplicates execution failed {0}".format(errcode))
shutil.move(self.output + ".dedup", self.output)
def markDuplicates(self):
cmd, stdout, stderr, errcode = COMPASSCFG["tools"]["picard"].execute(
source="path",
prepend="java -jar",
file="MarkDuplicates.jar",
append=
"I={0} O={1}.dedup METRICS_FILE=a.txt ASSUME_SORTED=true VERBOSITY=DEBUG VALIDATION_STRINGENCY=SILENT"
.format(self.output, self.output))
LE.debug(StringIO(stdout), "stdout")
LE.debug(StringIO(stderr), "stderr")
if errcode:
LE.critical("MarkDuplicates execution failed {0}".format(
md.returncode))
raise Exception("MarkDuplicates execution failed {0}".format(
md.returncode))
shutil.move(self.output + ".dedup", self.output)
parser.add_argument(i[0],
dest=i[1],
help=i[4],
default=False,
action='store_true')
else:
parser.add_argument(i[0], dest=i[1], help=i[4], default="DISABLED")
args = parser.parse_args()
try:
for i in FILTERS.availableFilters():
value = getattr(args, i[1])
if value and value != "DISABLED":
FILTERS.setUpFilter(i[1], value)
except ParameterError as e:
LE.critical("Parameter setup Error: {0}".format(e.message))
dump_exc()
try:
vcfFile = GormVcf(args.invcf)
FILTERS.filterVcf(vcfFile,
outvcf_path=args.outvcf,
outvcfIndel=args.outvcfIndel,
outfasta=args.outfasta,
stats=args.outstats,
guuid=args.guuid,
refid=args.ref_id)
print("Done")
except:
dump_exc()