def setUp(self):
signatures = [("GAC", "GAC"), ("AAA", "TTT"), ("CAA", "TTG")]
self.coder = Signature.SignatureCoder(signatures, 9)
self.test_seqs = [("GACAAAGACTTT", [1.0, 1.0, 0.0]),
("CAAAGACGACTTTAAATTT", [0.5, 1.0, 0.0]),
("AAATTTAAAGACTTTGAC", [1.0 / 3.0, 1.0, 0.0]),
("GACGAC", [1.0, 0.0, 0.0]),
("GACAAAAAAAAAGAC", [1.0, 0.0, 0.0]),
("GACAAAAAAAAAAGAC", [0.0, 0.0, 0.0])]
def setUp(self):
test_file = os.path.join('NeuralNetwork', 'enolase.fasta')
self.test_records = []
# load the records
handle = open(test_file, 'r')
self.test_records = list(
SeqIO.parse(handle, "fasta", alphabet=IUPAC.unambiguous_dna))
handle.close()
self.sig_finder = Signature.SignatureFinder()
def setUp(self):
test_file = os.path.join('NeuralNetwork', 'enolase.fasta')
self.test_records = []
# load the records
handle = open(test_file, 'r')
seq_parser = Fasta.SequenceParser(alphabet=IUPAC.unambiguous_dna)
iterator = Fasta.Iterator(handle, seq_parser)
while 1:
seq_record = iterator.next()
if seq_record is None:
break
self.test_records.append(seq_record)
handle.close()
self.sig_finder = Signature.SignatureFinder()
def test_inconsistent_signature_sizes(self):
with self.assertRaises(ValueError):
Signature.SignatureCoder([('GAC', 'GAC'), ('AA', 'TTT')], 1)