def testTestCase(self):
hmm = HMM()
hmm.train(self.small_train)
log.info(hmm)
hmm.log_transform()
# test
test_output = []
for seq in self.small_test:
test_output.append(hmm.viterbi(seq))
self.assertEqual(self.small_output, test_output)
def main():
parser = argparse.ArgumentParser(
description = (" Train a HMM to detect exon/intron gaps "),
)
parser.add_argument("--train", help="path to training data file", default="./test/small_training.fa")
parser.add_argument("--test", help="path to testing data file", default="./test/small_test.fa")
opts = parser.parse_args()
hmm = HMM()
# train
training_wheels = read_data(opts.train)
hmm.train(training_wheels)
print hmm
hmm.log_transform()
# test
testing_seqs = read_data(opts.test)
for seq in testing_seqs:
print hmm.log_viterbi(seq)
