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)
def __init__(self):
self.pfam = PFAM()
pass
class EvaluateHMMs(object):
def __init__(self):
self.pfam = PFAM()
pass
def translateSixFramesGenerator(self, bioseq, table=11):
revseq = bioseq.reverse_complement()
for i in range(3):
yield bioseq[i:].translate(table)
yield revseq[i:].translate(table)
def translateSixFrames(self, genomeId):
print(' Creating six frame translation.')
outFile = open('./hmm_test/' + genomeId + '.six_frames.fna', 'w')
contigFile = open(IMG.genomeDir + genomeId + '/' + genomeId + '.fna')
for rec in SeqIO.parse(contigFile, 'fasta'):
frameNumber = 0
for frame in self.translateSixFramesGenerator(rec.seq):
frameNumber += 1
SeqIO.write(
SeqRecord(frame,
description='',
id=rec.id + "_" + str(frameNumber)), outFile,
'fasta')
outFile.close()
def runPFAM(self, genomeId):
print(' Running PFAM HMMs.')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./hmm_test/'
+ genomeId + '.pfam.table.txt ./hmm/pfam_markers.hmm ' +
IMG.genomeDir + genomeId + '/' + genomeId +
'.genes.derep.faa > ./hmm_test/' + genomeId + '.pfam.tsv\n')
def runTIGRFAM(self, genomeId):
print(' Running TIGRFAM HMMs.')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./hmm_test/'
+ genomeId + '.tigr.table.txt ./hmm/tigr_markers.hmm ' +
IMG.genomeDir + genomeId + '/' + genomeId +
'.genes.faa > ./hmm_test/' + genomeId + '.tigr.tsv\n')
def runPFAM_SixFrames(self, genomeId):
print(' Running PFAM HMMs on six frame translation.')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./hmm_test/'
+ genomeId +
'.pfam.table.six_frames.txt ./hmm/pfam_markers.hmm ./hmm_test/' +
genomeId + '.six_frames.fna > ./hmm_test/' + genomeId +
'.pfam.six_frames.tsv\n')
def runTIGRFAM_SixFrames(self, genomeId):
print(' Running TIGRFAM HMMs on six frame translation.')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./hmm_test/'
+ genomeId +
'.tigr.table.six_frames.txt ./hmm/tigr_markers.hmm ./hmm_test/' +
genomeId + '.six_frames.fna > ./hmm_test/' + genomeId +
'.tigr.six_frames.tsv\n')
def readImgTable(self, genomeId, markers, extension, clusterIdIndex):
hits = {}
bHeader = True
for line in open(IMG.genomeDir + genomeId + '/' + genomeId +
extension):
if bHeader:
bHeader = False
continue
lineSplit = line.split('\t')
clusterId = lineSplit[clusterIdIndex]
if clusterId in markers:
s = hits.get(clusterId, set())
s.add(lineSplit[0])
hits[clusterId] = s
return hits
def readHmmTable(self, genomeId, extension):
hits = {}
for line in open('./hmm_test/' + genomeId + extension):
if line[0] == '#' or line.strip() == '':
continue
lineSplit = line.split()
clusterId = lineSplit[4]
if 'PF' in clusterId:
clusterId = clusterId.replace('PF', 'pfam')
clusterId = clusterId[0:clusterId.rfind('.')]
geneId = lineSplit[0]
evalue = float(lineSplit[12]) # i-evalue
start = int(lineSplit[17]) # seq. start
end = int(lineSplit[18]) # seq. end
hits[geneId] = hits.get(geneId,
[]) + [[clusterId, evalue, start, end]]
return hits
def compareResults(self, genomeId, pfamMarkers, tigrMarkers, fout):
# get marker hits to genes as determined by IMG
imgPfamHits = self.readImgTable(genomeId, pfamMarkers,
'.pfam.tab.txt', 8)
imgTigrHits = self.readImgTable(genomeId, tigrMarkers,
'.tigrfam.tab.txt', 6)
print(' PFAM IMG hits: ' + str(len(imgPfamHits)))
print(' PFAM TIGR hits: ' + str(len(imgTigrHits)))
# get marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable(genomeId, '.pfam.table.txt')
hmmTigrHits = self.readHmmTable(genomeId, '.tigr.table.txt')
print(' PFAM HMM hits: ' + str(len(hmmPfamHits)))
print(' TIGR HMM hits: ' + str(len(hmmTigrHits)))
# remove overlapping PFAM hits from the same clan
print(' Filtering PFAM hits from the same clan.')
filteredHmmPfamHits = self.pfam.filterHitsFromSameClan(
hmmPfamHits, pfamMarkers)
print(' Filtered PFAM hits: ' + str(len(filteredHmmPfamHits)))
# reform TIGR hits so dictionary is indexed by TIGR ids
reformedHmmTigrHits = {}
for geneId, hits in hmmTigrHits.items():
for h in hits:
tigrId = h[0]
s = reformedHmmTigrHits.get(tigrId, set())
s.add(geneId)
reformedHmmTigrHits[tigrId] = s
# compare results
pfamDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for pfamId in pfamMarkers:
if len(imgPfamHits.get(pfamId, set())) - len(
filteredHmmPfamHits.get(pfamId, set())) > 0:
imgAdditions += len(imgPfamHits.get(pfamId, set())) - len(
filteredHmmPfamHits.get(pfamId, set()))
if len(filteredHmmPfamHits.get(pfamId, set())) - len(
imgPfamHits.get(pfamId, set())) > 0:
hmmAdditions += len(filteredHmmPfamHits.get(
pfamId, set())) - len(imgPfamHits.get(pfamId, set()))
pfamDiff += len(
imgPfamHits.get(pfamId, set()).symmetric_difference(
filteredHmmPfamHits.get(pfamId, set())))
totalImgHits += len(imgPfamHits.get(pfamId, set()))
totalHmmHits += len(filteredHmmPfamHits.get(pfamId, set()))
print(
' PFAM (symmetric diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(pfamDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions))
fout.write(
' PFAM (diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(pfamDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions) + '\n')
tigrDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for tigrId in tigrMarkers:
if len(imgTigrHits.get(tigrId, set())) - len(
reformedHmmTigrHits.get(tigrId, set())) > 0:
imgAdditions += len(imgTigrHits.get(tigrId, set())) - len(
reformedHmmTigrHits.get(tigrId, set()))
if len(reformedHmmTigrHits.get(tigrId, set())) - len(
imgTigrHits.get(tigrId, set())) > 0:
hmmAdditions += len(reformedHmmTigrHits.get(
tigrId, set())) - len(imgTigrHits.get(tigrId, set()))
tigrDiff += len(
imgTigrHits.get(tigrId, set()).symmetric_difference(
reformedHmmTigrHits.get(tigrId, set())))
totalImgHits += len(imgTigrHits.get(tigrId, set()))
totalHmmHits += len(reformedHmmTigrHits.get(tigrId, set()))
print(
' TIGR (symmetric diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(tigrDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions))
print('')
fout.write(
' TIGR (diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(tigrDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions) + '\n\n')
def compareSixFrameResults(self, genomeId, pfamMarkers, tigrMarkers,
fout):
# get marker hits to genes as determined by IMG
imgPfamHits = self.readImgTable(genomeId, pfamMarkers,
'.pfam.tab.txt', 8)
imgTigrHits = self.readImgTable(genomeId, tigrMarkers,
'.tigrfam.tab.txt', 6)
# get marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable(genomeId, pfamMarkers,
'.pfam.table.six_frames.txt')
hmmTigrHits = self.readHmmTable(genomeId, tigrMarkers,
'.tigr.table.six_frames.txt')
# compare results
pfamDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for pfamId in pfamMarkers:
if len(imgPfamHits.get(pfamId, set())) - len(
hmmPfamHits.get(pfamId, set())) > 0:
imgAdditions += len(imgPfamHits.get(pfamId, set())) - len(
hmmPfamHits.get(pfamId, set()))
if len(hmmPfamHits.get(pfamId, set())) - len(
imgPfamHits.get(pfamId, set())) > 0:
hmmAdditions += len(hmmPfamHits.get(pfamId, set())) - len(
imgPfamHits.get(pfamId, set()))
pfamDiff += abs(
len(imgPfamHits.get(pfamId, set())) -
len(hmmPfamHits.get(pfamId, set())))
totalImgHits += len(imgPfamHits.get(pfamId, set()))
totalHmmHits += len(hmmPfamHits.get(pfamId, set()))
print(
' PFAM (diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(pfamDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions))
fout.write(
' PFAM (diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(pfamDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions) + '\n')
tigrDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for tigrId in tigrMarkers:
if len(imgTigrHits.get(tigrId, set())) - len(
hmmTigrHits.get(tigrId, set())) > 0:
imgAdditions += len(imgTigrHits.get(tigrId, set())) - len(
hmmTigrHits.get(tigrId, set()))
if len(hmmTigrHits.get(tigrId, set())) - len(
imgTigrHits.get(tigrId, set())) > 0:
hmmAdditions += len(hmmTigrHits.get(tigrId, set())) - len(
imgTigrHits.get(tigrId, set()))
tigrDiff += abs(
len(imgTigrHits.get(tigrId, set())) -
len(hmmTigrHits.get(tigrId, set())))
totalImgHits += len(imgTigrHits.get(tigrId, set()))
totalHmmHits += len(hmmTigrHits.get(tigrId, set()))
print(
' TIGR (diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(tigrDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions))
print('')
fout.write(
' TIGR (diff, IMG hits, HMM hits, IMG additional, HMM additional): '
+ str(tigrDiff) + ', ' + str(totalImgHits) + ', ' +
str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' +
str(hmmAdditions) + '\n\n')
def run(self):
img = IMG()
fout = open('./data/evaluate_hmms_with_prodigal.txt', 'w', 1)
# get list of all marker genes
markerset = MarkerSet()
pfamMarkers, tigrMarkers = markerset.getCalculatedMarkerGenes()
print('PFAM marker genes: ' + str(len(tigrMarkers)))
print('TIGR marker genes: ' + str(len(pfamMarkers)))
print('')
# run HMMs on each of the finished genomes
genomeIds = img.genomeIds('Finished')
for genomeId in genomeIds:
print(genomeId + ':')
fout.write(genomeId + ':\n')
self.runPFAM(genomeId)
self.runTIGRFAM(genomeId)
fout.write(' ORF results:\n')
self.compareResults(genomeId, pfamMarkers, tigrMarkers, fout)
#self.translateSixFrames(genomeId)
#self.runPFAM_SixFrames(genomeId)
#self.runTIGRFAM_SixFrames(genomeId)
#fout.write(' Six-frame translation results:\n')
#self.compareSixFrameResults(genomeId, pfamMarkers, tigrMarkers, fout)
fout.close()
def __init__(self):
self.pfam = PFAM()
pass
class EvaluateHMMs(object):
def __init__(self):
self.pfam = PFAM()
pass
def translateSixFramesGenerator(self, bioseq, table=11):
revseq = bioseq.reverse_complement()
for i in range(3):
yield bioseq[i:].translate(table)
yield revseq[i:].translate(table)
def translateSixFrames(self, genomeId):
print ' Creating six frame translation.'
outFile = open('./hmm_test/' + genomeId + '.six_frames.fna', 'w')
contigFile = open(IMG.genomeDir + genomeId + '/' + genomeId + '.fna')
for rec in SeqIO.parse(contigFile, 'fasta'):
frameNumber = 0
for frame in self.translateSixFramesGenerator(rec.seq):
frameNumber += 1
SeqIO.write(SeqRecord(frame, description='', id=rec.id + "_" + str(frameNumber)), outFile, 'fasta')
outFile.close()
def runPFAM(self, genomeId):
print ' Running PFAM HMMs.'
os.system('hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./hmm_test/' + genomeId + '.pfam.table.txt ./hmm/pfam_markers.hmm ' + IMG.genomeDir + genomeId + '/' + genomeId + '.genes.derep.faa > ./hmm_test/' + genomeId + '.pfam.tsv\n')
def runTIGRFAM(self, genomeId):
print ' Running TIGRFAM HMMs.'
os.system('hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./hmm_test/' + genomeId + '.tigr.table.txt ./hmm/tigr_markers.hmm ' + IMG.genomeDir + genomeId + '/' + genomeId + '.genes.faa > ./hmm_test/' + genomeId + '.tigr.tsv\n')
def runPFAM_SixFrames(self, genomeId):
print ' Running PFAM HMMs on six frame translation.'
os.system('hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./hmm_test/' + genomeId + '.pfam.table.six_frames.txt ./hmm/pfam_markers.hmm ./hmm_test/' + genomeId + '.six_frames.fna > ./hmm_test/' + genomeId + '.pfam.six_frames.tsv\n')
def runTIGRFAM_SixFrames(self, genomeId):
print ' Running TIGRFAM HMMs on six frame translation.'
os.system('hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./hmm_test/' + genomeId + '.tigr.table.six_frames.txt ./hmm/tigr_markers.hmm ./hmm_test/' + genomeId + '.six_frames.fna > ./hmm_test/' + genomeId + '.tigr.six_frames.tsv\n')
def readImgTable(self, genomeId, markers, extension, clusterIdIndex):
hits = {}
bHeader = True
for line in open(IMG.genomeDir + genomeId + '/' + genomeId + extension):
if bHeader:
bHeader = False
continue
lineSplit = line.split('\t')
clusterId = lineSplit[clusterIdIndex]
if clusterId in markers:
s = hits.get(clusterId, set())
s.add(lineSplit[0])
hits[clusterId] = s
return hits
def readHmmTable(self, genomeId, extension):
hits = {}
for line in open('./hmm_test/' + genomeId + extension):
if line[0] == '#' or line.strip() == '':
continue
lineSplit = line.split()
clusterId = lineSplit[4]
if 'PF' in clusterId:
clusterId = clusterId.replace('PF', 'pfam')
clusterId = clusterId[0:clusterId.rfind('.')]
geneId = lineSplit[0]
evalue = float(lineSplit[12]) # i-evalue
start = int(lineSplit[17]) # seq. start
end = int(lineSplit[18]) # seq. end
hits[geneId] = hits.get(geneId, []) + [[clusterId, evalue, start, end]]
return hits
def compareResults(self, genomeId, pfamMarkers, tigrMarkers, fout):
# get marker hits to genes as determined by IMG
imgPfamHits= self.readImgTable(genomeId, pfamMarkers, '.pfam.tab.txt', 8)
imgTigrHits = self.readImgTable(genomeId, tigrMarkers, '.tigrfam.tab.txt', 6)
print ' PFAM IMG hits: ' + str(len(imgPfamHits))
print ' PFAM TIGR hits: ' + str(len(imgTigrHits))
# get marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable(genomeId, '.pfam.table.txt')
hmmTigrHits = self.readHmmTable(genomeId, '.tigr.table.txt')
print ' PFAM HMM hits: ' + str(len(hmmPfamHits))
print ' TIGR HMM hits: ' + str(len(hmmTigrHits))
# remove overlapping PFAM hits from the same clan
print ' Filtering PFAM hits from the same clan.'
filteredHmmPfamHits = self.pfam.filterHitsFromSameClan(hmmPfamHits, pfamMarkers)
print ' Filtered PFAM hits: ' + str(len(filteredHmmPfamHits))
# reform TIGR hits so dictionary is indexed by TIGR ids
reformedHmmTigrHits = {}
for geneId, hits in hmmTigrHits.iteritems():
for h in hits:
tigrId = h[0]
s = reformedHmmTigrHits.get(tigrId, set())
s.add(geneId)
reformedHmmTigrHits[tigrId] = s
# compare results
pfamDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for pfamId in pfamMarkers:
if len(imgPfamHits.get(pfamId, set())) - len (filteredHmmPfamHits.get(pfamId, set())) > 0:
imgAdditions += len(imgPfamHits.get(pfamId, set())) - len (filteredHmmPfamHits.get(pfamId, set()))
if len(filteredHmmPfamHits.get(pfamId, set())) - len (imgPfamHits.get(pfamId, set())) > 0:
hmmAdditions += len(filteredHmmPfamHits.get(pfamId, set())) - len (imgPfamHits.get(pfamId, set()))
pfamDiff += len(imgPfamHits.get(pfamId, set()).symmetric_difference(filteredHmmPfamHits.get(pfamId, set())))
totalImgHits += len(imgPfamHits.get(pfamId, set()))
totalHmmHits += len(filteredHmmPfamHits.get(pfamId, set()))
print ' PFAM (symmetric diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(pfamDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions)
fout.write(' PFAM (diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(pfamDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions) + '\n')
tigrDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for tigrId in tigrMarkers:
if len(imgTigrHits.get(tigrId, set())) - len (reformedHmmTigrHits.get(tigrId, set())) > 0:
imgAdditions += len(imgTigrHits.get(tigrId, set())) - len (reformedHmmTigrHits.get(tigrId, set()))
if len(reformedHmmTigrHits.get(tigrId, set())) - len (imgTigrHits.get(tigrId, set())) > 0:
hmmAdditions += len(reformedHmmTigrHits.get(tigrId, set())) - len (imgTigrHits.get(tigrId, set()))
tigrDiff += len(imgTigrHits.get(tigrId, set()).symmetric_difference(reformedHmmTigrHits.get(tigrId, set())))
totalImgHits += len(imgTigrHits.get(tigrId, set()))
totalHmmHits += len(reformedHmmTigrHits.get(tigrId, set()))
print ' TIGR (symmetric diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(tigrDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions)
print ''
fout.write(' TIGR (diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(tigrDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions) + '\n\n')
def compareSixFrameResults(self, genomeId, pfamMarkers, tigrMarkers, fout):
# get marker hits to genes as determined by IMG
imgPfamHits= self.readImgTable(genomeId, pfamMarkers, '.pfam.tab.txt', 8)
imgTigrHits = self.readImgTable(genomeId, tigrMarkers, '.tigrfam.tab.txt', 6)
# get marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable(genomeId, pfamMarkers, '.pfam.table.six_frames.txt')
hmmTigrHits = self.readHmmTable(genomeId, tigrMarkers, '.tigr.table.six_frames.txt')
# compare results
pfamDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for pfamId in pfamMarkers:
if len(imgPfamHits.get(pfamId, set())) - len (hmmPfamHits.get(pfamId, set())) > 0:
imgAdditions += len(imgPfamHits.get(pfamId, set())) - len (hmmPfamHits.get(pfamId, set()))
if len(hmmPfamHits.get(pfamId, set())) - len (imgPfamHits.get(pfamId, set())) > 0:
hmmAdditions += len(hmmPfamHits.get(pfamId, set())) - len (imgPfamHits.get(pfamId, set()))
pfamDiff += abs(len(imgPfamHits.get(pfamId, set())) - len(hmmPfamHits.get(pfamId, set())))
totalImgHits += len(imgPfamHits.get(pfamId, set()))
totalHmmHits += len(hmmPfamHits.get(pfamId, set()))
print ' PFAM (diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(pfamDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions)
fout.write(' PFAM (diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(pfamDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions) + '\n')
tigrDiff = 0
totalImgHits = 0
totalHmmHits = 0
imgAdditions = 0
hmmAdditions = 0
for tigrId in tigrMarkers:
if len(imgTigrHits.get(tigrId, set())) - len (hmmTigrHits.get(tigrId, set())) > 0:
imgAdditions += len(imgTigrHits.get(tigrId, set())) - len (hmmTigrHits.get(tigrId, set()))
if len(hmmTigrHits.get(tigrId, set())) - len (imgTigrHits.get(tigrId, set())) > 0:
hmmAdditions += len(hmmTigrHits.get(tigrId, set())) - len (imgTigrHits.get(tigrId, set()))
tigrDiff += abs(len(imgTigrHits.get(tigrId, set())) - len(hmmTigrHits.get(tigrId, set())))
totalImgHits += len(imgTigrHits.get(tigrId, set()))
totalHmmHits += len(hmmTigrHits.get(tigrId, set()))
print ' TIGR (diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(tigrDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions)
print ''
fout.write(' TIGR (diff, IMG hits, HMM hits, IMG additional, HMM additional): ' + str(tigrDiff) + ', ' + str(totalImgHits) + ', ' + str(totalHmmHits) + ', ' + str(imgAdditions) + ', ' + str(hmmAdditions) + '\n\n')
def run(self):
img = IMG()
fout = open('./data/evaluate_hmms_with_prodigal.txt', 'w', 1)
# get list of all marker genes
markerset = MarkerSet()
pfamMarkers, tigrMarkers = markerset.getCalculatedMarkerGenes()
print 'PFAM marker genes: ' + str(len(tigrMarkers))
print 'TIGR marker genes: ' + str(len(pfamMarkers))
print ''
# run HMMs on each of the finished genomes
genomeIds = img.genomeIds('Finished')
for genomeId in genomeIds:
print genomeId + ':'
fout.write(genomeId + ':\n')
self.runPFAM(genomeId)
self.runTIGRFAM(genomeId)
fout.write(' ORF results:\n')
self.compareResults(genomeId, pfamMarkers, tigrMarkers, fout)
#self.translateSixFrames(genomeId)
#self.runPFAM_SixFrames(genomeId)
#self.runTIGRFAM_SixFrames(genomeId)
#fout.write(' Six-frame translation results:\n')
#self.compareSixFrameResults(genomeId, pfamMarkers, tigrMarkers, fout)
fout.close()