def __processBin(self, outDir, tableOut, hmmerOut, markerFile,
bKeepAlignment, bNucORFs, bCalledGenes, queueIn,
queueOut):
"""Thread safe bin processing."""
markerSetParser = MarkerSetParser(self.threadsPerSearch)
while True:
binFile = queueIn.get(block=True, timeout=None)
if binFile == None:
break
binId = binIdFromFilename(binFile)
binDir = os.path.join(outDir, 'bins', binId)
makeSurePathExists(binDir)
# run Prodigal
if not bCalledGenes:
prodigal = ProdigalRunner(binDir)
if not prodigal.areORFsCalled(bNucORFs):
prodigal.run(binFile, bNucORFs)
aaGeneFile = prodigal.aaGeneFile
else:
aaGeneFile = binFile
shutil.copyfile(
aaGeneFile, os.path.join(binDir,
DefaultValues.PRODIGAL_AA))
# extract HMMs into temporary file
hmmModelFile = markerSetParser.createHmmModelFile(
binId, markerFile)
# run HMMER
hmmer = HMMERRunner()
tableOutPath = os.path.join(binDir, tableOut)
hmmerOutPath = os.path.join(binDir, hmmerOut)
keepAlignStr = ''
if not bKeepAlignment:
keepAlignStr = '--noali'
hmmer.search(
hmmModelFile, aaGeneFile, tableOutPath, hmmerOutPath,
'--cpu ' + str(self.threadsPerSearch) +
' --notextw -E 0.1 --domE 0.1 ' + keepAlignStr, bKeepAlignment)
queueOut.put((binId, hmmModelFile))
def __processBin(self, outDir, tableOut, hmmerOut, markerFile, bKeepAlignment, bNucORFs, bCalledGenes, queueIn, queueOut):
"""Thread safe bin processing."""
markerSetParser = MarkerSetParser(self.threadsPerSearch)
while True:
binFile = queueIn.get(block=True, timeout=None)
if binFile == None:
break
binId = binIdFromFilename(binFile)
binDir = os.path.join(outDir, 'bins', binId)
makeSurePathExists(binDir)
# run Prodigal
if not bCalledGenes:
prodigal = ProdigalRunner(binDir)
if not prodigal.areORFsCalled(bNucORFs):
prodigal.run(binFile, bNucORFs)
aaGeneFile = prodigal.aaGeneFile
else:
aaGeneFile = binFile
shutil.copyfile(aaGeneFile, os.path.join(binDir, DefaultValues.PRODIGAL_AA))
# extract HMMs into temporary file
hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile)
# run HMMER
hmmer = HMMERRunner()
tableOutPath = os.path.join(binDir, tableOut)
hmmerOutPath = os.path.join(binDir, hmmerOut)
keepAlignStr = ''
if not bKeepAlignment:
keepAlignStr = '--noali'
hmmer.search(hmmModelFile, aaGeneFile, tableOutPath, hmmerOutPath,
'--cpu ' + str(self.threadsPerSearch) + ' --notextw -E 0.1 --domE 0.1 ' + keepAlignStr,
bKeepAlignment)
queueOut.put((binId, hmmModelFile))
