def process(filename_a, filename_b):
a = open(filename_a)
b = open(filename_b)
_, sequence_a = utils.load(a)
a.close()
_, sequence_b = utils.load(b)
b.close()
print(utils.compare(sequence_a, sequence_b))
def compare(filename_a, filename_b):
a = open(filename_a)
b = open(filename_b)
_, sequence_a = utils.load(a)
a.close()
_, sequence_b = utils.load(b)
b.close()
return utils.compare(sequence_a, sequence_b)
def process(in_filename, out_filename):
in_file = open(in_filename)
out_file = open(out_filename, 'w')
header, sequence = utils.load(in_file)
in_file.close()
out_file.write(header + '\n')
out_file.write('\n'.join(utils.prepare_subsequences(utils.translate(sequence), 80)))
out_file.close()
def load_test():
# Given
f = open('test.tmp')
# When
header, sequence = utils.load(f)
f.close()
# Then
assert header == '>header'
assert sequence == 'AGCTGC'
def process(model_file, sequence_file, window_size):
model = json.loads(model_file.read())
model_file.close()
header, sequence = utils.load(sequence_file)
sequence_file.close()
print(header)
hmm = HMM(**model['model'])
subsequences = utils.prepare_subsequences(sequence, window_size)
decoded = ''
for seq in subsequences:
decoded += ''.join(hmm.decode(seq)[1])
print('{} / {}'.format(len(decoded), 3 * len(sequence)), file=sys.stderr)
lines = utils.prepare_subsequences(decoded, 80)
for l in lines:
print(l)
def process(sequence_file):
header, sequence = utils.load(arguments['<fasta_sequence>'])
gene_sequence = utils.to_codon_sequence(sequence)
hmm = create_from_sequence(gene_sequence)
print(json.dumps({'header': header, 'model': hmm.__dict__}, sort_keys=True, indent=4, separators=(',', ': ')))