def __init__(self):
self.pfam = PFAM()
pass
def __init__(self):
self.pfam = PFAM()
pass
class EvaluateHMMs(object):
def __init__(self):
self.pfam = PFAM()
pass
def runProdigal(self, genomeId):
print(' Running Prodigal.')
os.system('time prodigal -m -c -f gff -g 11 -a ./prodigal_test/' +
genomeId + '.genes.faa -d ./prodigal_test/' + genomeId +
'.genes.fna -i ' + IMG.genomeDir + genomeId + '/' +
genomeId + '.fna > ./prodigal_test/' + genomeId +
'.prodigal.gff\n')
def runGeneMark(self, genomeId):
print(' Running GeneMarkS.')
os.system(
'time ~/apps/genemark/gmsuite/gmsn.pl --prok --format GFF --gcode 11 --name '
+ genomeId + ' --species ' + genomeId + ' --faa --fnn ' +
IMG.genomeDir + genomeId + '/' + genomeId + '.fna')
os.system('mv ' + genomeId + '.fna.faa ./genemark_test/' + genomeId +
'.genes.faa')
os.system('mv ' + genomeId + '.fna.fnn ./genemark_test/' + genomeId +
'.genes.fna')
os.system('mv ' + genomeId + '* ./genemark_test/')
def runPFAM(self, genomeId):
print(' Running PFAM HMMs.')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./genemark_test/'
+ genomeId +
'.pfam.table.txt ./hmm/pfam_markers.hmm ./genemark_test/' +
genomeId + '.genes.faa > ./genemark_test/' + genomeId +
'.pfam.tsv\n')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./prodigal_test/'
+ genomeId +
'.pfam.table.txt ./hmm/pfam_markers.hmm ./prodigal_test/' +
genomeId + '.genes.faa > ./prodigal_test/' + genomeId +
'.pfam.tsv\n')
def runTIGRFAM(self, genomeId):
print(' Running TIGR HMMs.')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./genemark_test/'
+ genomeId +
'.tigr.table.txt ./hmm/tigr_markers.hmm ./genemark_test/' +
genomeId + '.genes.faa > ./genemark_test/' + genomeId +
'.tigr.tsv\n')
os.system(
'hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./prodigal_test/'
+ genomeId +
'.tigr.table.txt ./hmm/tigr_markers.hmm ./prodigal_test/' +
genomeId + '.genes.faa > ./prodigal_test/' + genomeId +
'.tigr.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
for clusterId, geneSet in hits.items():
hits[clusterId] = len(geneSet)
return hits
def readHmmTable(self, resultsFile):
hits = {}
for line in open(resultsFile):
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 prodigal marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable('./prodigal_test/' + genomeId +
'.pfam.table.txt')
hmmTigrHits = self.readHmmTable('./prodigal_test/' + genomeId +
'.tigr.table.txt')
print(' Prodigal PFAM HMM hits: ' + str(len(hmmPfamHits)))
print(' Prodigal TIGR HMM hits: ' + str(len(hmmTigrHits)))
# remove overlapping PFAM hits from the same clan
print(' Filtering Prodigal PFAM hits from the same clan.')
filteredHmmPfamHits = self.pfam.filterHitsFromSameClan(
hmmPfamHits, pfamMarkers)
print(' Filtered Prodigal PFAM hits: ' +
str(len(filteredHmmPfamHits)))
# reformat filtered PFAM hits
prodigalPfamHits = {}
for pfamId, geneIds in filteredHmmPfamHits.items():
prodigalPfamHits[pfamId] = len(geneIds)
# reformat TIGR hits so dictionary is indexed by TIGR ids
prodigalTigrHits = {}
for _, hits in hmmTigrHits.items():
for h in hits:
tigrId = h[0]
prodigalTigrHits[tigrId] = prodigalTigrHits.get(tigrId, 0) + 1
# get GeneMark marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable('./genemark_test/' + genomeId +
'.pfam.table.txt')
hmmTigrHits = self.readHmmTable('./genemark_test/' + genomeId +
'.tigr.table.txt')
print(' GeneMark PFAM HMM hits: ' + str(len(hmmPfamHits)))
print(' GeneMark TIGR HMM hits: ' + str(len(hmmTigrHits)))
# remove overlapping PFAM hits from the same clan
print(' Filtering GeneMark PFAM hits from the same clan.')
filteredHmmPfamHits = self.pfam.filterHitsFromSameClan(
hmmPfamHits, pfamMarkers)
print(' Filtered GeneMark PFAM hits: ' +
str(len(filteredHmmPfamHits)))
# reformat filtered PFAM hits
genemarkPfamHits = {}
for pfamId, geneIds in filteredHmmPfamHits.items():
genemarkPfamHits[pfamId] = len(geneIds)
# reformat TIGR hits so dictionary is indexed by TIGR ids
genemarkTigrHits = {}
for _, hits in hmmTigrHits.items():
for h in hits:
tigrId = h[0]
genemarkTigrHits[tigrId] = genemarkTigrHits.get(tigrId, 0) + 1
# compare results
prodigalDiff = 0
genemarkDiff = 0
totalImgHits = 0
totalProdigalHits = 0
totalGeneMarkHits = 0
for pfamId in pfamMarkers:
prodigalDiff += abs(
prodigalPfamHits.get(pfamId, 0) - imgPfamHits.get(pfamId, 0))
genemarkDiff += abs(
genemarkPfamHits.get(pfamId, 0) - imgPfamHits.get(pfamId, 0))
totalImgHits += imgPfamHits.get(pfamId, 0)
totalProdigalHits += prodigalPfamHits.get(pfamId, 0)
totalGeneMarkHits += genemarkPfamHits.get(pfamId, 0)
print(
' PFAM (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): '
+ str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' +
str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' +
str(totalGeneMarkHits))
fout.write(
' PFAM (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): '
+ str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' +
str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' +
str(totalGeneMarkHits) + '\n')
prodigalDiff = 0
genemarkDiff = 0
totalImgHits = 0
totalProdigalHits = 0
totalGeneMarkHits = 0
for tigrId in tigrMarkers:
prodigalDiff += abs(
prodigalTigrHits.get(tigrId, 0) - imgTigrHits.get(tigrId, 0))
genemarkDiff += abs(
genemarkTigrHits.get(tigrId, 0) - imgTigrHits.get(tigrId, 0))
totalImgHits += imgTigrHits.get(tigrId, 0)
totalProdigalHits += prodigalTigrHits.get(tigrId, 0)
totalGeneMarkHits += genemarkTigrHits.get(tigrId, 0)
print(
' TIGR (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): '
+ str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' +
str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' +
str(totalGeneMarkHits))
print('')
fout.write(
' TIGR (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): '
+ str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' +
str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' +
str(totalGeneMarkHits) + '\n\n')
def run(self):
img = IMG()
fout = open('./data/evaluate_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.runProdigal(genomeId)
self.runGeneMark(genomeId)
self.runPFAM(genomeId)
self.runTIGRFAM(genomeId)
self.compareResults(genomeId, pfamMarkers, tigrMarkers, fout)
fout.close()
class EvaluateHMMs(object):
def __init__(self):
self.pfam = PFAM()
pass
def runProdigal(self, genomeId):
print ' Running Prodigal.'
os.system('time prodigal -m -c -f gff -g 11 -a ./prodigal_test/' + genomeId + '.genes.faa -d ./prodigal_test/' + genomeId + '.genes.fna -i ' + IMG.genomeDir + genomeId + '/' + genomeId + '.fna > ./prodigal_test/' + genomeId + '.prodigal.gff\n')
def runGeneMark(self, genomeId):
print ' Running GeneMarkS.'
os.system('time ~/apps/genemark/gmsuite/gmsn.pl --prok --format GFF --gcode 11 --name ' + genomeId + ' --species ' + genomeId + ' --faa --fnn ' + IMG.genomeDir + genomeId + '/' + genomeId + '.fna')
os.system('mv ' + genomeId + '.fna.faa ./genemark_test/' + genomeId + '.genes.faa')
os.system('mv ' + genomeId + '.fna.fnn ./genemark_test/' + genomeId + '.genes.fna')
os.system('mv ' + genomeId + '* ./genemark_test/')
def runPFAM(self, genomeId):
print ' Running PFAM HMMs.'
os.system('hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./genemark_test/' + genomeId + '.pfam.table.txt ./hmm/pfam_markers.hmm ./genemark_test/' + genomeId + '.genes.faa > ./genemark_test/' + genomeId + '.pfam.tsv\n')
os.system('hmmsearch --notextw --noali --cpu 0 --cut_ga --domtblout ./prodigal_test/' + genomeId + '.pfam.table.txt ./hmm/pfam_markers.hmm ./prodigal_test/' + genomeId + '.genes.faa > ./prodigal_test/' + genomeId + '.pfam.tsv\n')
def runTIGRFAM(self, genomeId):
print ' Running TIGR HMMs.'
os.system('hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./genemark_test/' + genomeId + '.tigr.table.txt ./hmm/tigr_markers.hmm ./genemark_test/' + genomeId + '.genes.faa > ./genemark_test/' + genomeId + '.tigr.tsv\n')
os.system('hmmsearch --notextw --noali --cpu 0 --cut_nc --domtblout ./prodigal_test/' + genomeId + '.tigr.table.txt ./hmm/tigr_markers.hmm ./prodigal_test/' + genomeId + '.genes.faa > ./prodigal_test/' + genomeId + '.tigr.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
for clusterId, geneSet in hits.iteritems():
hits[clusterId] = len(geneSet)
return hits
def readHmmTable(self, resultsFile):
hits = {}
for line in open(resultsFile):
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 prodigal marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable('./prodigal_test/' + genomeId + '.pfam.table.txt')
hmmTigrHits = self.readHmmTable('./prodigal_test/' + genomeId + '.tigr.table.txt')
print ' Prodigal PFAM HMM hits: ' + str(len(hmmPfamHits))
print ' Prodigal TIGR HMM hits: ' + str(len(hmmTigrHits))
# remove overlapping PFAM hits from the same clan
print ' Filtering Prodigal PFAM hits from the same clan.'
filteredHmmPfamHits = self.pfam.filterHitsFromSameClan(hmmPfamHits, pfamMarkers)
print ' Filtered Prodigal PFAM hits: ' + str(len(filteredHmmPfamHits))
# reformat filtered PFAM hits
prodigalPfamHits = {}
for pfamId, geneIds in filteredHmmPfamHits.iteritems():
prodigalPfamHits[pfamId] = len(geneIds)
# reformat TIGR hits so dictionary is indexed by TIGR ids
prodigalTigrHits = {}
for _, hits in hmmTigrHits.iteritems():
for h in hits:
tigrId = h[0]
prodigalTigrHits[tigrId] = prodigalTigrHits.get(tigrId, 0) + 1
# get GeneMark marker hits to genes as determined by HMMs
hmmPfamHits = self.readHmmTable('./genemark_test/' + genomeId + '.pfam.table.txt')
hmmTigrHits = self.readHmmTable('./genemark_test/' + genomeId + '.tigr.table.txt')
print ' GeneMark PFAM HMM hits: ' + str(len(hmmPfamHits))
print ' GeneMark TIGR HMM hits: ' + str(len(hmmTigrHits))
# remove overlapping PFAM hits from the same clan
print ' Filtering GeneMark PFAM hits from the same clan.'
filteredHmmPfamHits = self.pfam.filterHitsFromSameClan(hmmPfamHits, pfamMarkers)
print ' Filtered GeneMark PFAM hits: ' + str(len(filteredHmmPfamHits))
# reformat filtered PFAM hits
genemarkPfamHits = {}
for pfamId, geneIds in filteredHmmPfamHits.iteritems():
genemarkPfamHits[pfamId] = len(geneIds)
# reformat TIGR hits so dictionary is indexed by TIGR ids
genemarkTigrHits = {}
for _, hits in hmmTigrHits.iteritems():
for h in hits:
tigrId = h[0]
genemarkTigrHits[tigrId] = genemarkTigrHits.get(tigrId, 0) + 1
# compare results
prodigalDiff = 0
genemarkDiff = 0
totalImgHits = 0
totalProdigalHits = 0
totalGeneMarkHits = 0
for pfamId in pfamMarkers:
prodigalDiff += abs(prodigalPfamHits.get(pfamId, 0) - imgPfamHits.get(pfamId, 0))
genemarkDiff += abs(genemarkPfamHits.get(pfamId, 0) - imgPfamHits.get(pfamId, 0))
totalImgHits += imgPfamHits.get(pfamId, 0)
totalProdigalHits += prodigalPfamHits.get(pfamId, 0)
totalGeneMarkHits += genemarkPfamHits.get(pfamId, 0)
print ' PFAM (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): ' + str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' + str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' + str(totalGeneMarkHits)
fout.write(' PFAM (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): ' + str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' + str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' + str(totalGeneMarkHits) + '\n')
prodigalDiff = 0
genemarkDiff = 0
totalImgHits = 0
totalProdigalHits = 0
totalGeneMarkHits = 0
for tigrId in tigrMarkers:
prodigalDiff += abs(prodigalTigrHits.get(tigrId, 0) - imgTigrHits.get(tigrId, 0))
genemarkDiff += abs(genemarkTigrHits.get(tigrId, 0) - imgTigrHits.get(tigrId, 0))
totalImgHits += imgTigrHits.get(tigrId, 0)
totalProdigalHits += prodigalTigrHits.get(tigrId, 0)
totalGeneMarkHits += genemarkTigrHits.get(tigrId, 0)
print ' TIGR (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): ' + str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' + str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' + str(totalGeneMarkHits)
print ''
fout.write(' TIGR (Prodigal diff, GeneMark diff, IMG hits, Prodigal hits, GeneMark hits): ' + str(prodigalDiff) + ', ' + str(genemarkDiff) + ', ' + str(totalImgHits) + ', ' + str(totalProdigalHits) + ', ' + str(totalGeneMarkHits) + '\n\n')
def run(self):
img = IMG()
fout = open('./data/evaluate_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.runProdigal(genomeId)
self.runGeneMark(genomeId)
self.runPFAM(genomeId)
self.runTIGRFAM(genomeId)
self.compareResults(genomeId, pfamMarkers, tigrMarkers, fout)
fout.close()
