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()
