def __runHmmAlign(self, allTrustedGenomeIds, genesInGenomes, outputGeneDir,
outputModelDir, queueIn, queueOut):
"""Run each marker gene in a separate thread."""
while True:
markerId = queueIn.get(block=True, timeout=None)
if markerId == None:
break
modelName = markerId
if modelName.startswith('pfam'):
modelName = modelName.replace('pfam', 'PF')
markerSeqFile = os.path.join(outputGeneDir, modelName + '.faa')
fout = open(markerSeqFile, 'w')
for genomeId in allTrustedGenomeIds:
seqs = readFasta(IMG.genomeDir + '/' + genomeId + '/' +
genomeId + '.genes.faa')
for geneId in genesInGenomes[genomeId].get(markerId, []):
fout.write('>' + genomeId + '|' + geneId + '\n')
fout.write(seqs[geneId] + '\n')
fout.close()
hmmer = HMMERRunner('align')
hmmer.align(os.path.join(outputModelDir, modelName + '.hmm'),
markerSeqFile,
os.path.join(outputGeneDir, modelName + '.aln.faa'),
trim=False,
outputFormat='Pfam')
self.__maskAlignment(
os.path.join(outputGeneDir, modelName + '.aln.faa'),
os.path.join(outputGeneDir, modelName + '.aln.masked.faa'))
queueOut.put(modelName)
def __alignMarker(self, markerId, binSeqs, binStats, bReportHitStats, alignOutputDir, hmmModelFile, bKeepUnmaskedAlign):
unalignSeqFile = os.path.join(alignOutputDir, markerId + '.unaligned.faa')
fout = open(unalignSeqFile, 'w')
numSeqs = 0
for binId, seqs in binSeqs.iteritems():
for seqId, seq in seqs.iteritems():
header = '>' + binId + DefaultValues.SEQ_CONCAT_CHAR + seqId
if bReportHitStats:
header += ' [e-value=%.4g,score=%.1f]' % (binStats[binId][seqId][0], binStats[binId][seqId][1])
fout.write(header + '\n')
fout.write(seq + '\n')
numSeqs += 1
fout.close()
if numSeqs > 0:
alignSeqFile = os.path.join(alignOutputDir, markerId + '.aligned.faa')
HA = HMMERRunner(mode='align')
HA.align(hmmModelFile, unalignSeqFile, alignSeqFile, writeMode='>', outputFormat=self.outputFormat, trim=False)
makedSeqFile = os.path.join(alignOutputDir, markerId + '.masked.faa')
self.__maskAlignment(alignSeqFile, makedSeqFile)
if not bKeepUnmaskedAlign:
os.remove(alignSeqFile)
os.remove(unalignSeqFile)
def __alignMarker(self, markerId, binSeqs, binStats, bReportHitStats, alignOutputDir, hmmModelFile, bKeepUnmaskedAlign):
unalignSeqFile = os.path.join(alignOutputDir, markerId + '.unaligned.faa')
fout = open(unalignSeqFile, 'w')
numSeqs = 0
for binId, seqs in binSeqs.items():
for seqId, seq in seqs.items():
header = '>' + binId + DefaultValues.SEQ_CONCAT_CHAR + seqId
if bReportHitStats:
header += ' [e-value=%.4g,score=%.1f]' % (binStats[binId][seqId][0], binStats[binId][seqId][1])
fout.write(header + '\n')
fout.write(seq + '\n')
numSeqs += 1
fout.close()
if numSeqs > 0:
alignSeqFile = os.path.join(alignOutputDir, markerId + '.aligned.faa')
HA = HMMERRunner(mode='align')
HA.align(hmmModelFile, unalignSeqFile, alignSeqFile, writeMode='>', outputFormat=self.outputFormat, trim=False)
makedSeqFile = os.path.join(alignOutputDir, markerId + '.masked.faa')
self.__maskAlignment(alignSeqFile, makedSeqFile)
if not bKeepUnmaskedAlign:
os.remove(alignSeqFile)
os.remove(unalignSeqFile)
def __runHmmAlign(self, genomeIds, genesInGenomes, outputGeneDir, outputModelDir, queueIn, queueOut):
"""Run each marker gene in a separate thread."""
while True:
markerId = queueIn.get(block=True, timeout=None)
if markerId == None:
break
modelName = markerId
if modelName.startswith('pfam'):
modelName = modelName.replace('pfam', 'PF')
markerSeqFile = os.path.join(outputGeneDir, modelName + '.faa')
fout = open(markerSeqFile, 'w')
for genomeId in genomeIds:
seqs = readFasta(IMG.genomeDir + '/' + genomeId + '/' + genomeId + '.genes.faa')
for geneId in genesInGenomes[genomeId].get(markerId, []):
if geneId not in seqs:
# this shouldn't be necessary, but the IMG metadata isn't always
# perfectly in sync with the sequence data
continue
fout.write('>' + genomeId + '|' + geneId + '\n')
fout.write(seqs[geneId] + '\n')
fout.close()
hmmer = HMMERRunner('align')
hmmer.align(os.path.join(outputModelDir, modelName + '.hmm'), markerSeqFile, os.path.join(outputGeneDir, modelName + '.aln.faa'), trim=False, outputFormat='Pfam')
self.__maskAlignment(os.path.join(outputGeneDir, modelName + '.aln.faa'), os.path.join(outputGeneDir, modelName + '.aln.masked.faa'))
queueOut.put(modelName)
def __runHmmAlign(self, allTrustedGenomeIds, genesInGenomes, outputGeneDir, outputModelDir, queueIn, queueOut):
"""Run each marker gene in a separate thread."""
while True:
markerId = queueIn.get(block=True, timeout=None)
if markerId == None:
break
modelName = markerId
if modelName.startswith('pfam'):
modelName = modelName.replace('pfam', 'PF')
markerSeqFile = os.path.join(outputGeneDir, modelName + '.faa')
fout = open(markerSeqFile, 'w')
for genomeId in allTrustedGenomeIds:
seqs = readFasta(IMG.genomeDir + '/' + genomeId + '/' + genomeId + '.genes.faa')
for geneId in genesInGenomes[genomeId].get(markerId, []):
fout.write('>' + genomeId + '|' + geneId + '\n')
fout.write(seqs[geneId] + '\n')
fout.close()
hmmer = HMMERRunner('align')
hmmer.align(os.path.join(outputModelDir, modelName + '.hmm'), markerSeqFile, os.path.join(outputGeneDir, modelName + '.aln.faa'), trim=False, outputFormat='Pfam')
self.__maskAlignment(os.path.join(outputGeneDir, modelName + '.aln.faa'), os.path.join(outputGeneDir, modelName + '.aln.masked.faa'))
queueOut.put(modelName)
def __runHmmAlign(self, genomeIds, genesInGenomes, outputGeneDir,
outputModelDir, queueIn, queueOut):
"""Run each marker gene in a separate thread."""
while True:
markerId = queueIn.get(block=True, timeout=None)
if markerId == None:
break
modelName = markerId
if modelName.startswith('pfam'):
modelName = modelName.replace('pfam', 'PF')
markerSeqFile = os.path.join(outputGeneDir, modelName + '.faa')
fout = open(markerSeqFile, 'w')
for genomeId in genomeIds:
seqs = readFasta(IMG.genomeDir + '/' + genomeId + '/' +
genomeId + '.genes.faa')
for geneId in genesInGenomes[genomeId].get(markerId, []):
if geneId not in seqs:
# this shouldn't be necessary, but the IMG metadata isn't always
# perfectly in sync with the sequence data
continue
fout.write('>' + genomeId + '|' + geneId + '\n')
fout.write(seqs[geneId] + '\n')
fout.close()
hmmer = HMMERRunner('align')
hmmer.align(os.path.join(outputModelDir, modelName + '.hmm'),
markerSeqFile,
os.path.join(outputGeneDir, modelName + '.aln.faa'),
trim=False,
outputFormat='Pfam')
self.__maskAlignment(
os.path.join(outputGeneDir, modelName + '.aln.faa'),
os.path.join(outputGeneDir, modelName + '.aln.masked.faa'))
queueOut.put(modelName)
