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 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()