def cleanUpExecution( self, cmd, stdout, stderr, errcode ):
"""
Args:
cmd:
stdout:
stderr:
errcode:
"""
LE.debug(StringIO(stdout))
if errcode:
LE.error(StringIO(stderr))
raise Exception(
"CMD [{0}] exit with status [{1}]".format(cmd, errcode))
def execCommand( self, cmd ):
"""
Args:
cmd:
"""
origcmd = cmd
LE.debug("Running command: [{0}]".format(cmd))
cmd = shlex.split(cmd)
p = subprocess.Popen(cmd, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
errcode = p.wait()
LE.debug(StringIO(stdout))
if errcode:
LE.error(StringIO(stderr))
raise Exception(
"CMD [{0}] exit with status [{1}]".format(origcmd, errcode))
def map(self):
for i in self.readgroups:
fq1 = self.tmpdir + "/" + i + "-A.fq"
fq2 = self.tmpdir + "/" + i + "-B.fq"
output = open(self.tmpdir + "/" + i + ".sam", "w")
p = COMPASSCFG["tools"]["bwa"].popen(
append="mem -R '@RG\\tID:{0}' {1} {2} {3} -L 20 -B 3 -O 6 -T 20"
.format(i, self.ref, fq1, fq2),
stderr=subprocess.PIPE,
stdout=output)
self.commandsHistory.append(p.cmd)
LE.debug(p.stderr, "stderr")
errcode = p.wait()
if errcode:
LE.error("BWA tool failed")
raise Exception("BWA tool failed")
os.unlink(fq1)
os.unlink(fq2)
output = self.tmpdir + "/" + i + ".sam"
self.insertsizes[i] = self.generateSeqStats(output)
if not args.fq1 or (args.fq2 and args.shuffled):
print(
"You must specify at least one FastQ File(fq1). If you specify two -s parameter is not compatible"
)
sys.exit(0)
if args.header:
LE.info("Reading header from {0}".format(args.header))
if args.rgroup == "UNKNOWN":
head = open(args.header).read()
if '@RG' in head:
args.rgroup = re.findall(
"[0-9a-z]{8}-[0-9a-z]{4}-[0-9a-z]{4}-[0-9a-z]{4}-[0-9a-z]{12}",
head, re.I)[0]
else:
LE.error("Can not find read group on header file")
md = COMPASSCFG['tools']['samtools'].popen(
append="view -h -S -b -o {0} -".format(args.output),
stderr=subprocess.PIPE,
stdin=subprocess.PIPE)
SamFile = Fq2Sam(open(args.header).read(),
args.rgroup,
args.fq1,
args.fq2,
md.stdin,
shuffled=args.shuffled)
else:
try:
rg, pl, lib, sn, cn = args.headerinfo.split(",")
except:
LE.error(
def dumpStdError(self):
self.stderror.seek(0)
LE.error(self.stderror)