def _sortbam(self, unsortedBamFile, sortedBamFile, nproc):
"""Sort unsortedBamFile and output sortedBamFile."""
if not sortedBamFile.endswith(".bam"):
raise ValueError("sorted bam file name %s must end with .bam" %
sortedBamFile)
sortedPrefix = sortedBamFile[0:-4]
cmd = 'samtools --version||true'
_samtoolsversion = ["0", "1", "19"]
try:
_out, _code, _msg = Execute(self.name, cmd)
if "samtools" in _out[0]:
_samtoolsversion = str(_out[0][8:]).strip().split('.')
else:
pass
except Exception:
pass
_stvmajor = int(_samtoolsversion[0])
if _stvmajor >= 1:
cmd = 'samtools sort --threads {t} -m 4G -o {sortedBamFile} {unsortedBamFile}'.format(
t=nproc,
sortedBamFile=sortedBamFile,
unsortedBamFile=unsortedBamFile)
else:
cmd = 'samtools sort --threads {t} -m 4G {unsortedBamFile} {prefix}'.format(
t=nproc, unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)
Execute(self.name, cmd)
def _sortbam(self, unsortedBamFile, sortedBamFile):
"""Sort unsortedBamFile and output sortedBamFile."""
if not sortedBamFile.endswith(".bam"):
raise ValueError("sorted bam file name %s must end with .bam" %
sortedBamFile)
sortedPrefix = sortedBamFile[0:-4]
cmd = 'samtools --version'
_samtoolsversion = ["0","1","19"]
try:
_out, _code, _msg = Execute(self.name, cmd)
if "samtools" in _out[0]:
_samtoolsversion = str(_out[0][8:]).strip().split('.')
else:
pass
except Exception:
pass
logging.info(self.name + ": blah %s %s %s" % (_out, _code, _msg))
logging.info(self.name + ": samtoolsversion %s %s %s" % (_samtoolsversion[0],_samtoolsversion[1],_samtoolsversion[2]))
_stvmajor = int(_samtoolsversion[0])
if _stvmajor >= 1:
cmd = 'samtools sort -m 4G -o {sortedBamFile} {unsortedBamFile}'.format(
sortedBamFile=sortedBamFile, unsortedBamFile=unsortedBamFile)
else:
cmd = 'samtools sort -m 4G {unsortedBamFile} {prefix}'.format(
unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)
Execute(self.name, cmd)
def _makebai(self, sortedBamFile, outBaiFile):
"""Build *.bai index file."""
cmd = 'samtools --version'
_samtoolsversion = ["0", "1", "19"]
try:
_out, _code, _msg = Execute(self.name, cmd)
if "samtools" in _out[0]:
_samtoolsversion = str(_out[0][8:]).strip().split('.')
else:
pass
except Exception:
pass
_stvmajor = int(_samtoolsversion[0])
_stvminor = int(_samtoolsversion[1])
if _stvmajor == 1 and _stvminor == 2:
# only for 1.2
cmd = "samtools index {sortedBamFile}".format(
sortedBamFile=sortedBamFile)
else:
cmd = "samtools index {sortedBamFile} {outBaiFile}".format(
sortedBamFile=sortedBamFile, outBaiFile=outBaiFile)
Execute(self.name, cmd)
def _makepbi(self, sortedBamFile):
"""Generate *.pbi PacBio BAM index."""
cmd = "pbindex %s" % sortedBamFile
Execute(self.name, cmd)
def _execute(self):
"""Execute a command (self.cmd)."""
return Execute(self.name, self.cmd)