Пример #1
0
        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()
Пример #2
0
        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()