def __workerThread(self, ubiquityThreshold, singleCopyThreshold,
minGenomes, colocatedDistThreshold,
colocatedGenomeThreshold, metadata, queueIn, queueOut):
"""Process each data item in parallel."""
img = IMG('/srv/whitlam/bio/db/checkm/img/img_metadata.tsv',
'/srv/whitlam/bio/db/checkm/pfam/tigrfam2pfam.tsv')
markerSetBuilder = MarkerSetBuilder()
while True:
lineage = queueIn.get(block=True, timeout=None)
if lineage == None:
break
if lineage == 'Universal':
genomeIds = img.genomeIdsByTaxonomy('prokaryotes', metadata)
else:
genomeIds = img.genomeIdsByTaxonomy(lineage, metadata)
if len(genomeIds) >= minGenomes:
markerSet = markerSetBuilder.buildMarkerSet(
genomeIds, ubiquityThreshold, singleCopyThreshold,
colocatedDistThreshold)
colocatedSets = markerSet.markerSet
else:
colocatedSets = None
# allow results to be processed or written to file
queueOut.put((lineage, colocatedSets, len(genomeIds)))
def __workerThread(self, ubiquityThreshold, singleCopyThreshold,
minGenomes,
colocatedDistThreshold, colocatedGenomeThreshold,
metadata,
queueIn, queueOut):
"""Process each data item in parallel."""
img = IMG('/srv/whitlam/bio/db/checkm/img/img_metadata.tsv', '/srv/whitlam/bio/db/checkm/pfam/tigrfam2pfam.tsv')
markerSetBuilder = MarkerSetBuilder()
while True:
lineage = queueIn.get(block=True, timeout=None)
if lineage == None:
break
if lineage == 'Universal':
genomeIds = img.genomeIdsByTaxonomy('prokaryotes', metadata)
else:
genomeIds = img.genomeIdsByTaxonomy(lineage, metadata)
if len(genomeIds) >= minGenomes:
markerSet = markerSetBuilder.buildMarkerSet(genomeIds, ubiquityThreshold, singleCopyThreshold, colocatedDistThreshold)
colocatedSets = markerSet.markerSet
else:
colocatedSets = None
# allow results to be processed or written to file
queueOut.put((lineage, colocatedSets, len(genomeIds)))
def __getUniversalMarkerGenes(self, phyloUbiquityThreshold,
phyloSingleCopyThreshold, outputGeneDir):
img = IMG('/srv/whitlam/bio/db/checkm/img/img_metadata.tsv',
'/srv/whitlam/bio/db/checkm/pfam/tigrfam2pfam.tsv')
markerSetBuilder = MarkerSetBuilder()
metadata = img.genomeMetadata()
allTrustedGenomeIds = set()
phyloMarkerGenes = {}
for lineage in ['Archaea', 'Bacteria']:
# get all genomes in lineage
print('\nIdentifying all ' + lineage + ' genomes.')
trustedGenomeIds = img.genomeIdsByTaxonomy(lineage, metadata)
print(' Trusted genomes in lineage: ' +
str(len(trustedGenomeIds)))
if len(trustedGenomeIds) < 1:
print(
' Skipping lineage due to insufficient number of genomes.'
)
continue
allTrustedGenomeIds.update(trustedGenomeIds)
print(' Building marker set.')
markerGenes = markerSetBuilder.buildMarkerGenes(
trustedGenomeIds, phyloUbiquityThreshold,
phyloSingleCopyThreshold)
phyloMarkerGenes[lineage] = markerGenes
#print lineage
#print len(markerGenes)
#print 'pfam01379: ', ('pfam01379' in markerGenes)
#print '--------------------'
# universal marker genes
universalMarkerGenes = None
for markerGenes in list(phyloMarkerGenes.values()):
if universalMarkerGenes == None:
universalMarkerGenes = markerGenes
else:
universalMarkerGenes.intersection_update(markerGenes)
fout = open(os.path.join(outputGeneDir, 'phylo_marker_set.txt'), 'w')
fout.write(str(universalMarkerGenes))
fout.close()
print('')
print(' Universal marker genes: ' + str(len(universalMarkerGenes)))
return allTrustedGenomeIds, universalMarkerGenes
def __getUniversalMarkerGenes(self, phyloUbiquityThreshold, phyloSingleCopyThreshold, outputGeneDir):
img = IMG('/srv/whitlam/bio/db/checkm/img/img_metadata.tsv', '/srv/whitlam/bio/db/checkm/pfam/tigrfam2pfam.tsv')
markerSetBuilder = MarkerSetBuilder()
metadata = img.genomeMetadata()
allTrustedGenomeIds = set()
phyloMarkerGenes = {}
for lineage in ['Archaea', 'Bacteria']:
# get all genomes in lineage
print '\nIdentifying all ' + lineage + ' genomes.'
trustedGenomeIds = img.genomeIdsByTaxonomy(lineage, metadata)
print ' Trusted genomes in lineage: ' + str(len(trustedGenomeIds))
if len(trustedGenomeIds) < 1:
print ' Skipping lineage due to insufficient number of genomes.'
continue
allTrustedGenomeIds.update(trustedGenomeIds)
print ' Building marker set.'
markerGenes = markerSetBuilder.buildMarkerGenes(trustedGenomeIds, phyloUbiquityThreshold, phyloSingleCopyThreshold)
phyloMarkerGenes[lineage] = markerGenes
#print lineage
#print len(markerGenes)
#print 'pfam01379: ', ('pfam01379' in markerGenes)
#print '--------------------'
# universal marker genes
universalMarkerGenes = None
for markerGenes in phyloMarkerGenes.values():
if universalMarkerGenes == None:
universalMarkerGenes = markerGenes
else:
universalMarkerGenes.intersection_update(markerGenes)
fout = open(os.path.join(outputGeneDir, 'phylo_marker_set.txt'), 'w')
fout.write(str(universalMarkerGenes))
fout.close()
print ''
print ' Universal marker genes: ' + str(len(universalMarkerGenes))
return allTrustedGenomeIds, universalMarkerGenes