def test_realpath(self):
"""Test real_upath and real_ppath."""
print real_upath("ref with space")
self.assertTrue(real_upath("ref with space").endswith("ref\ with\ space"))
self.assertTrue(real_upath("ref\ with\ space").endswith("ref\ with\ space"))
self.assertTrue(real_ppath("ref with space").endswith("ref with space"))
self.assertTrue(real_ppath("ref\ with\ space").endswith("ref with space"))
def _output(self, inSam, refFile, outFile, readType=None, smrtTitle=False):
"""Generate a SAM, BAM or a CMP.H5 file.
Input:
inSam : an input SAM/BAM file. (e.g. fileName.filteredSam)
refFile : the reference file. (e.g. fileName.targetFileName)
outFile : the output SAM/BAM or CMP.H5 file.
(i.e. fileName.outputFileName)
readType: standard or cDNA or CCS (can be None if not specified)
Output:
output, errCode, errMsg
"""
output, errCode, errMsg = "", 0, ""
outFormat = getFileFormat(outFile)
if outFormat == FILE_FORMATS.BAM:
pass # Nothing to be done
if outFormat == FILE_FORMATS.SAM:
logging.info("OutputService: Genearte the output SAM file.")
logging.debug("OutputService: Move {src} as {dst}".format(
src=inSam, dst=outFile))
try:
shutil.move(real_ppath(inSam), real_ppath(outFile))
except shutil.Error as e:
output, errCode, errMsg = "", 1, str(e)
elif outFormat == FILE_FORMATS.CMP:
#`samtoh5 inSam outFile -readType readType
logging.info("OutputService: Genearte the output CMP.H5 " +
"file using samtoh5.")
prog = "samtoh5"
cmd = "samtoh5 {samFile} {refFile} {outFile}".format(
samFile=inSam, refFile=refFile, outFile=outFile)
if readType is not None:
cmd += " -readType {0} ".format(readType)
if smrtTitle:
cmd += " -smrtTitle "
# Execute the command line
logging.debug("OutputService: Call \"{0}\"".format(cmd))
output, errCode, errMsg = backticks(cmd)
elif outFormat == FILE_FORMATS.XML:
logging.info(
"OutputService: Generating the output XML file".format(
samFile=inSam, outFile=outFile))
# Create {out}.xml, given {out}.bam
outBam = str(outFile[0:-3]) + "bam"
aln = None
# FIXME This should really be more automatic
if self.args.readType == "CCS":
self._output_dataset_type = ConsensusAlignmentSet
aln = self._output_dataset_type(real_ppath(outBam))
for res in aln.externalResources:
res.reference = refFile
aln.write(outFile)
if errCode != 0:
errMsg = prog + " returned a non-zero exit status." + errMsg
logging.error(errMsg)
raise RuntimeError(errMsg)
return output, errCode, errMsg
def _output(self, inSam, refFile, outFile, readType=None, smrtTitle=False):
"""Generate a SAM, BAM or a CMP.H5 file.
Input:
inSam : an input SAM/BAM file. (e.g. fileName.filteredSam)
refFile : the reference file. (e.g. fileName.targetFileName)
outFile : the output SAM/BAM or CMP.H5 file.
(i.e. fileName.outputFileName)
readType: standard or cDNA or CCS (can be None if not specified)
Output:
output, errCode, errMsg
"""
output, errCode, errMsg = "", 0, ""
outFormat = getFileFormat(outFile)
if outFormat == FILE_FORMATS.BAM:
pass # Nothing to be done
if outFormat == FILE_FORMATS.SAM:
logging.info("OutputService: Genearte the output SAM file.")
logging.debug("OutputService: Move {src} as {dst}".format(
src=inSam, dst=outFile))
try:
shutil.move(real_ppath(inSam), real_ppath(outFile))
except shutil.Error as e:
output, errCode, errMsg = "", 1, str(e)
elif outFormat == FILE_FORMATS.CMP:
#`samtoh5 inSam outFile -readType readType
logging.info("OutputService: Genearte the output CMP.H5 " +
"file using samtoh5.")
prog = "samtoh5"
cmd = "samtoh5 {samFile} {refFile} {outFile}".format(
samFile=inSam, refFile=refFile, outFile=outFile)
if readType is not None:
cmd += " -readType {0} ".format(readType)
if smrtTitle:
cmd += " -smrtTitle "
# Execute the command line
logging.debug("OutputService: Call \"{0}\"".format(cmd))
output, errCode, errMsg = backticks(cmd)
elif outFormat == FILE_FORMATS.XML:
logging.info("OutputService: Generating the output XML file".
format(samFile=inSam, outFile=outFile))
# Create {out}.xml, given {out}.bam
outBam = str(outFile[0:-3]) + "bam"
aln = None
# FIXME This should really be more automatic
if self.args.readType == "CCS":
self._output_dataset_type = ConsensusAlignmentSet
aln = self._output_dataset_type(real_ppath(outBam))
for res in aln.externalResources:
res.reference = refFile
aln.write(outFile)
if errCode != 0:
errMsg = prog + " returned a non-zero exit status." + errMsg
logging.error(errMsg)
raise RuntimeError(errMsg)
return output, errCode, errMsg
def test_realpath(self):
"""Test real_upath and real_ppath."""
print real_upath("ref with space")
self.assertTrue(
real_upath("ref with space").endswith("ref\ with\ space"))
self.assertTrue(
real_upath("ref\ with\ space").endswith("ref\ with\ space"))
self.assertTrue(
real_ppath("ref with space").endswith("ref with space"))
self.assertTrue(
real_ppath("ref\ with\ space").endswith("ref with space"))
def _output(self, inSam, refFile, outFile, readType=None):
"""Generate a SAM, BAM file.
Input:
inSam : an input SAM/BAM file. (e.g. fileName.filteredSam)
refFile : the reference file. (e.g. fileName.targetFileName)
outFile : the output SAM/BAM file
(i.e. fileName.outputFileName)
readType: standard or cDNA or CCS (can be None if not specified)
Output:
output, errCode, errMsg
"""
output, errCode, errMsg = "", 0, ""
outFormat = getFileFormat(outFile)
if outFormat == FILE_FORMATS.BAM:
pass # Nothing to be done
if outFormat == FILE_FORMATS.SAM:
logging.info("OutputService: Genearte the output SAM file.")
logging.debug("OutputService: Move %s as %s", inSam, outFile)
try:
shutil.move(real_ppath(inSam), real_ppath(outFile))
except shutil.Error as e:
output, errCode, errMsg = "", 1, "Exited with error: " + str(e)
logging.error(errMsg)
raise RuntimeError(errMsg)
elif outFormat == FILE_FORMATS.CMP:
errMsg = "pbalign no longer supports CMP.H5 Output in 3.0."
logging.error(errMsg)
raise IOError(errMsg)
elif outFormat == FILE_FORMATS.XML:
logging.info("OutputService: Generating the output XML file %s %s",
inSam, outFile)
# Create {out}.xml, given {out}.bam
outBam = str(outFile[0:-3]) + "bam"
aln = None
# FIXME This should really be more automatic
if readType == "CCS":
self._output_dataset_type = ConsensusAlignmentSet
aln = self._output_dataset_type(real_ppath(outBam))
for res in aln.externalResources:
res.reference = refFile
aln.write(outFile)
return output, errCode, errMsg
def _output(self, inSam, refFile, outFile, readType=None):
"""Generate a SAM, BAM file.
Input:
inSam : an input SAM/BAM file. (e.g. fileName.filteredSam)
refFile : the reference file. (e.g. fileName.targetFileName)
outFile : the output SAM/BAM file
(i.e. fileName.outputFileName)
readType: standard or cDNA or CCS (can be None if not specified)
Output:
output, errCode, errMsg
"""
output, errCode, errMsg = "", 0, ""
outFormat = getFileFormat(outFile)
if outFormat == FILE_FORMATS.BAM:
pass # Nothing to be done
if outFormat == FILE_FORMATS.SAM:
logging.info("OutputService: Genearte the output SAM file.")
logging.debug("OutputService: Move %s as %s", inSam, outFile)
try:
shutil.move(real_ppath(inSam), real_ppath(outFile))
except shutil.Error as e:
output, errCode, errMsg = "", 1, "Exited with error: " + str(e)
logging.error(errMsg)
raise RuntimeError(errMsg)
elif outFormat == FILE_FORMATS.CMP:
errMsg = "pbalign no longer supports CMP.H5 Output in 3.0."
logging.error(errMsg)
raise IOError(errMsg)
elif outFormat == FILE_FORMATS.XML:
logging.info("OutputService: Generating the output XML file %s %s",
inSam, outFile)
# Create {out}.xml, given {out}.bam
outBam = str(outFile[0:-3]) + "bam"
aln = None
# FIXME This should really be more automatic
if readType == "CCS":
self._output_dataset_type = ConsensusAlignmentSet
aln = self._output_dataset_type(real_ppath(outBam))
for res in aln.externalResources:
res.reference = refFile
aln.write(outFile)
return output, errCode, errMsg
def _output(self, inSam, refFile, outFile, readType=None, smrtTitle=False):
"""Generate a sam or a cmp.h5 file.
Input:
inSam : an input SAM file. (e.g. fileName.filteredSam)
refFile : the reference file. (e.g. fileName.targetFileName)
outFile : the output SAM or CMP.H5 file.
(i.e. fileName.outputFileName)
readType: standard or cDNA or CCS (can be None if not specified)
Output:
output, errCode, errMsg
"""
output, errCode, errMsg = "", 0, ""
if getFileFormat(outFile) == FILE_FORMATS.SAM:
#`mv inSam outFile`
logging.info("OutputService: Genearte the output SAM file.")
logging.debug("OutputService: Move {src} as {dst}".format(
src=inSam, dst=outFile))
try:
shutil.move(real_ppath(inSam), real_ppath(outFile))
except shutil.Error as e:
output, errCode, errMsg = "", 1, str(e)
elif getFileFormat(outFile) == FILE_FORMATS.CMP:
#`samtoh5 inSam outFile -readType readType
logging.info("OutputService: Genearte the output CMP.H5 " +
"file using samtoh5.")
prog = "samtoh5"
cmd = "samtoh5 {samFile} {refFile} {outFile}".format(
samFile=inSam, refFile=refFile, outFile=outFile)
if readType is not None:
cmd += " -readType {0} ".format(readType)
if smrtTitle:
cmd += " -smrtTitle "
# Execute the command line
logging.debug("OutputService: Call \"{0}\"".format(cmd))
output, errCode, errMsg = backticks(cmd)
if errCode != 0:
errMsg = prog + " returned a non-zero exit status." + errMsg
logging.error(errMsg)
raise RuntimeError(errMsg)
return output, errCode, errMsg