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')