def __createMarkerHMMs(self, binMarkerSet, outputFile, bReportProgress=True):
"""Create HMM file for markers."""
# get list of marker genes
markerGenes = binMarkerSet.getMarkerGenes()
# get all genes from the same clan as any marker gene
pfam = PFAM(DefaultValues.PFAM_CLAN_FILE)
genesInSameClan = pfam.genesInSameClan(markerGenes)
# extract marker genes along with all genes from the same clan
allMarkers = markerGenes | genesInSameClan
if bReportProgress:
self.logger.info(" There are %d genes in the marker set and %d genes from the same PFAM clan." % (len(markerGenes), len(genesInSameClan)))
# create file with all model accession numbers
keyFile = os.path.join(tempfile.gettempdir(), str(uuid.uuid4()))
fout = open(keyFile, 'w')
for modelAcc in allMarkers:
fout.write(modelAcc + '\n')
fout.close()
# fetch specified models
HF = HMMERRunner(mode='fetch')
HF.fetch(DefaultValues.HMM_MODELS, keyFile, outputFile, bKeyFile=True)
# index the HMM file
if os.path.exists(outputFile + '.ssi'):
os.remove(outputFile + '.ssi')
HF.index(outputFile)
# remove key file
os.remove(keyFile)
def __createMarkerHMMs(self, binMarkerSet, outputFile, bReportProgress=True):
"""Create HMM file for markers."""
# get list of marker genes
markerGenes = binMarkerSet.getMarkerGenes()
# get all genes from the same clan as any marker gene
pfam = PFAM(DefaultValues.PFAM_CLAN_FILE)
genesInSameClan = pfam.genesInSameClan(markerGenes)
# extract marker genes along with all genes from the same clan
allMarkers = markerGenes | genesInSameClan
if bReportProgress:
self.logger.info(" There are %d genes in the marker set and %d genes from the same PFAM clan." % (len(markerGenes), len(genesInSameClan)))
# create file with all model accession numbers
keyFile = os.path.join(tempfile.gettempdir(), str(uuid.uuid4()))
fout = open(keyFile, 'w')
for modelAcc in allMarkers:
fout.write(modelAcc + '\n')
fout.close()
# fetch specified models
HF = HMMERRunner(mode='fetch')
HF.fetch(DefaultValues.HMM_MODELS, keyFile, outputFile, bKeyFile=True)
# index the HMM file
if os.path.exists(outputFile + '.ssi'):
os.remove(outputFile + '.ssi')
HF.index(outputFile)
# remove key file
os.remove(keyFile)
def run(self):
# read all taxonomic-specific marker genes
print('Reading taxonomic-specific marker genes.')
taxonomicMarkers = set()
taxonParser = TaxonParser()
taxonMarkerSets = taxonParser.readMarkerSets()
for _, taxa in taxonMarkerSets.items():
for _, markerSet in taxa.items():
taxonomicMarkers = taxonomicMarkers.union(
markerSet.getMarkerGenes())
print(' Taxonomic-specific marker genes: %d' % len(taxonomicMarkers))
# read all lineage-specific marker genes
print('Reading lineage-specific marker genes.')
lineageMarkers = set()
treeParser = TreeParser()
uniqueIdToLineageStatistics = treeParser.readNodeMetadata()
for uniqueId, d in uniqueIdToLineageStatistics.items():
markerSet = MarkerSet(uniqueId, 'NA', int(d['# genomes']),
eval(d['marker set']))
lineageMarkers = lineageMarkers.union(markerSet.getMarkerGenes())
print(' Lineage-specific marker genes: %d' % len(lineageMarkers))
# gather all marker genes
markerGenes = taxonomicMarkers.union(lineageMarkers)
print(' Total marker genes: %d' % len(markerGenes))
# get genes from same clan as marker genes
print('Gathering HMMs from the same clan as marker genes.')
pfam = PFAM()
genesInSameClan = pfam.genesInSameClan(markerGenes)
allMarkers = markerGenes.union(genesInSameClan)
# create file with all model accession numbers
keyFile = os.path.join(tempfile.gettempdir(), str(uuid.uuid4()))
fout = open(keyFile, 'w')
for modelAcc in allMarkers:
fout.write(modelAcc + '\n')
fout.close()
# fetch specified models
HF = HMMERRunner(mode='fetch')
HF.fetch(self.hmms, keyFile, self.outputHMMs, bKeyFile=True)
# index the HMM file
if os.path.exists(self.outputHMMs + '.ssi'):
os.remove(self.outputHMMs + '.ssi')
HF.index(self.outputHMMs)
# remove key file
os.remove(keyFile)
def run(self):
# read all taxonomic-specific marker genes
print 'Reading taxonomic-specific marker genes.'
taxonomicMarkers = set()
taxonParser = TaxonParser()
taxonMarkerSets = taxonParser.readMarkerSets()
for _, taxa in taxonMarkerSets.iteritems():
for _, markerSet in taxa.iteritems():
taxonomicMarkers = taxonomicMarkers.union(markerSet.getMarkerGenes())
print ' Taxonomic-specific marker genes: %d' % len(taxonomicMarkers)
# read all lineage-specific marker genes
print 'Reading lineage-specific marker genes.'
lineageMarkers = set()
treeParser = TreeParser()
uniqueIdToLineageStatistics = treeParser.readNodeMetadata()
for uniqueId, d in uniqueIdToLineageStatistics.iteritems():
markerSet = MarkerSet(uniqueId, 'NA', int(d['# genomes']), eval(d['marker set']))
lineageMarkers = lineageMarkers.union(markerSet.getMarkerGenes())
print ' Lineage-specific marker genes: %d' % len(lineageMarkers)
# gather all marker genes
markerGenes = taxonomicMarkers.union(lineageMarkers)
print ' Total marker genes: %d' % len(markerGenes)
# get genes from same clan as marker genes
print 'Gathering HMMs from the same clan as marker genes.'
pfam = PFAM()
genesInSameClan = pfam.genesInSameClan(markerGenes)
allMarkers = markerGenes.union(genesInSameClan)
# create file with all model accession numbers
keyFile = os.path.join(tempfile.gettempdir(), str(uuid.uuid4()))
fout = open(keyFile, 'w')
for modelAcc in allMarkers:
fout.write(modelAcc + '\n')
fout.close()
# fetch specified models
HF = HMMERRunner(mode='fetch')
HF.fetch(self.hmms, keyFile, self.outputHMMs, bKeyFile=True)
# index the HMM file
if os.path.exists(self.outputHMMs + '.ssi'):
os.remove(self.outputHMMs + '.ssi')
HF.index(self.outputHMMs)
# remove key file
os.remove(keyFile)