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()
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()
def run(self, minGenomes, minMarkerSets):
img = IMG()
pfam = PFAM()
# get list of all marker genes
markerset = MarkerSet()
pfamIds, tigrIds = markerset.getCalculatedMarkerGenes()
print 'TIGR marker genes: ' + str(len(tigrIds))
print 'PFAM marker genes: ' + str(len(pfamIds))
# get all PFAM HMMs that are in the same clan
# as any of the marker genes
pfamIdToClanId = pfam.pfamIdToClanId()
clans = set()
for pfamId in pfamIds:
if pfamId.replace('PF', 'pfam') in pfamIdToClanId:
clans.add(pfamIdToClanId[pfamId])
for pfamId, clanId in pfamIdToClanId.iteritems():
if clanId in clans:
pfamIds.add(pfamId)
print ' PFAM HMMs require to cover marker gene clans: ' + str(
len(pfamIds))
# get name of each PFAM HMM
fout = open('./hmm/pfam.keyfile.txt', 'w')
pfamNames = []
for line in open(img.pfamHMMs):
if 'NAME' in line:
name = line[line.find(' '):].strip()
elif 'ACC' in line:
acc = line[line.find(' '):line.rfind('.')].strip()
if acc.replace('PF', 'pfam') in pfamIds:
pfamNames.append(name)
fout.write(name + '\n')
fout.close()
print 'PFAM names: ' + str(len(pfamNames))
# extract each PFAM HMM
os.system('hmmfetch -f ' + img.pfamHMMs +
' ./hmm/pfam.keyfile.txt > ./hmm/pfam_markers.hmm')
# get name of each PFAM HMM
fout = open('./hmm/tigr.keyfile.txt', 'w')
for tigrId in tigrIds:
fout.write(tigrId + '\n')
fout.close()
# extract each PFAM HMM
os.system('hmmfetch -f ' + img.tigrHMMs +
' ./hmm/tigr.keyfile.txt > ./hmm/tigr_markers.hmm')
def run(self, minGenomes, minMarkerSets):
img = IMG()
pfam = PFAM()
# get list of all marker genes
markerset = MarkerSet()
pfamIds, tigrIds = markerset.getCalculatedMarkerGenes()
print 'TIGR marker genes: ' + str(len(tigrIds))
print 'PFAM marker genes: ' + str(len(pfamIds))
# get all PFAM HMMs that are in the same clan
# as any of the marker genes
pfamIdToClanId = pfam.pfamIdToClanId()
clans = set()
for pfamId in pfamIds:
if pfamId.replace('PF', 'pfam') in pfamIdToClanId:
clans.add(pfamIdToClanId[pfamId])
for pfamId, clanId in pfamIdToClanId.iteritems():
if clanId in clans:
pfamIds.add(pfamId)
print ' PFAM HMMs require to cover marker gene clans: ' + str(len(pfamIds))
# get name of each PFAM HMM
fout = open('./hmm/pfam.keyfile.txt', 'w')
pfamNames = []
for line in open(img.pfamHMMs):
if 'NAME' in line:
name = line[line.find(' '):].strip()
elif 'ACC' in line:
acc = line[line.find(' '):line.rfind('.')].strip()
if acc.replace('PF', 'pfam') in pfamIds:
pfamNames.append(name)
fout.write(name + '\n')
fout.close()
print 'PFAM names: ' + str(len(pfamNames))
# extract each PFAM HMM
os.system('hmmfetch -f ' + img.pfamHMMs + ' ./hmm/pfam.keyfile.txt > ./hmm/pfam_markers.hmm')
# get name of each PFAM HMM
fout = open('./hmm/tigr.keyfile.txt', 'w')
for tigrId in tigrIds:
fout.write(tigrId + '\n')
fout.close()
# extract each PFAM HMM
os.system('hmmfetch -f ' + img.tigrHMMs + ' ./hmm/tigr.keyfile.txt > ./hmm/tigr_markers.hmm')
