def main(base_fname, base_dir): src = os.path.join(base_dir, base_fname) tmpf = os.path.join(base_dir, 'realigned/' + base_fname + '.selected.fa') dst = os.path.join( base_dir, 'realigned/' + os.path.splitext(base_fname)[0] + '.{}_{}.muscle.fa' ) sequences = ['sequence1', 'sequence2', 'sequence3'] for x in range(len(sequences)-1): for y in range(x+1, len(sequences)): sX = sequences[x] sY = sequences[y] if sX != sY: select_sequences(src, tmpf, [sequences[x], sequences[y]]) dest = dst.format(sX, sY) os.system("muscle -in {inp} -out {out} 2> /dev/null".format( inp=tmpf, out=dest, )) if len(sequences) == 3: print 'Transitivity: ' + str(transitivitycheck.score(dst)) sX = sequences[0] sY = sequences[1] print 'Equality: ' + str( transitivitycheck.compare_with_source(src, dst.format(sX, sY), sX, sY) ) os.remove(tmpf)
def main(base_fname, base_dir): src = os.path.join(base_dir, base_fname) tmpf = os.path.join(base_dir, 'realigned/' + base_fname + '.selected.fa') dst = os.path.join( base_dir, 'realigned/' + os.path.splitext(base_fname)[0] + '.{}_{}.muscle.fa') sequences = ['sequence1', 'sequence2', 'sequence3'] for x in range(len(sequences) - 1): for y in range(x + 1, len(sequences)): sX = sequences[x] sY = sequences[y] if sX != sY: select_sequences(src, tmpf, [sequences[x], sequences[y]]) dest = dst.format(sX, sY) os.system("muscle -in {inp} -out {out} 2> /dev/null".format( inp=tmpf, out=dest, )) if len(sequences) == 3: print 'Transitivity: ' + str(transitivitycheck.score(dst)) sX = sequences[0] sY = sequences[1] print 'Equality: ' + str( transitivitycheck.compare_with_source(src, dst.format(sX, sY), sX, sY)) os.remove(tmpf)
def main(base_filename='simulated_alignment', base_dir='data/sequences'): # models = ['SimpleHMM2.js', 'ClassificationHMM.js', 'OracleHMM.js'] # models = ['SimpleHMM2.js'] # models = ['ClassificationHMM.js', 'OracleHMM.js'] # models = ['SimpleHMM2Bio.js', 'ClassificationHMMBio.js', 'OracleHMMBio.js'] # models = ['SimpleHMM2Test.js', 'ClassificationHMMTest.js', 'OracleHMMTest.js'] # models = ['SimpleHMM2Test.js'] models = ['OracleCHMM.js'] # models = ['OracleHMMTest.js'] # models = ['ClassificationHMMBio.js']#, 'OracleHMMBio.js'] src = os.path.join(base_dir, base_filename) sequences = ['sequence1', 'sequence2', 'sequence3'] # sequences = ['sequence1', 'sequence2'] for model in models: dst = os.path.join( base_dir, 'realigned/' + path.splitext(base_filename)[0] + '.{}_{}.' + model + '.fa') threads = list() for x in range(len(sequences) - 1): for y in range(x + 1, len(sequences)): sX = sequences[x] sY = sequences[y] if sX != sY: dest = dst.format(sX, sY) threads.append( threading.Thread(target=realign, args=(src, dest, sX, sY, model))) for t in threads: t.start() for t in threads: t.join() print model if len(sequences) == 3: print 'Transitivity: ' + str(transitivitycheck.score(dst)) sX = sequences[0] sY = sequences[1] print 'Equality: ' + str( transitivitycheck.compare_with_source(src, dst.format(sX, sY), sX, sY)) sys.stdout.flush()
def main(base_filename='simulated_alignment', base_dir='data/sequences'): # models = ['SimpleHMM2.js', 'ClassificationHMM.js', 'OracleHMM.js'] # models = ['SimpleHMM2.js'] # models = ['ClassificationHMM.js', 'OracleHMM.js'] # models = ['SimpleHMM2Bio.js', 'ClassificationHMMBio.js', 'OracleHMMBio.js'] # models = ['SimpleHMM2Test.js', 'ClassificationHMMTest.js', 'OracleHMMTest.js'] # models = ['SimpleHMM2Test.js'] models = ['OracleCHMM.js'] # models = ['OracleHMMTest.js'] # models = ['ClassificationHMMBio.js']#, 'OracleHMMBio.js'] src = os.path.join(base_dir, base_filename) sequences = ['sequence1', 'sequence2', 'sequence3'] # sequences = ['sequence1', 'sequence2'] for model in models: dst = os.path.join( base_dir, 'realigned/' + path.splitext(base_filename)[0] + '.{}_{}.' + model + '.fa' ) threads = list() for x in range(len(sequences)-1): for y in range(x+1, len(sequences)): sX = sequences[x] sY = sequences[y] if sX != sY: dest = dst.format(sX, sY) threads.append( threading.Thread(target=realign, args=(src, dest, sX, sY, model)) ) for t in threads: t.start() for t in threads: t.join() print model if len(sequences) == 3: print 'Transitivity: ' + str(transitivitycheck.score(dst)) sX = sequences[0] sY = sequences[1] print 'Equality: ' + str( transitivitycheck.compare_with_source(src, dst.format(sX, sY), sX, sY) ) sys.stdout.flush()