def test_minimal_parser(self):
"""MinimalFastaParser should read single record as (label, seq) tuple"""
seqs = list(MinimalPhylipParser(self.big_interleaved))
self.assertEqual(len(seqs), 10)
label, seq = seqs[-1]
self.assertEqual(label, 'Frog')
self.assertEqual(seq, \
'ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA')
self.assertEqual(seqs[0][0], 'Cow')
seqs = list(MinimalPhylipParser(self.space_interleaved))
self.assertEqual(len(seqs), 5)
self.assertEqual(seqs[0][0], 'cox2_leita')
self.assertEqual(seqs[-1][0], 'cox2_tborr')
self.assertEqual(len(seqs[0][1]), 176)
self.assertEqual(len(seqs[-1][1]), 176)
seqs = list(MinimalPhylipParser(self.interleaved_little))
self.assertEqual(len(seqs), 6)
self.assertEqual(seqs[1][0], 'Hesperorni')
self.assertEqual(seqs[-1][0], 'B.subtilis')
self.assertEqual(seqs[-1][1], 'GGCAGCCAATCACGGCAGCCAATCACGGCAGCCAATCAC')
seqs = list(MinimalPhylipParser(self.noninterleaved_little))
self.assertEqual(len(seqs), 6)
self.assertEqual(seqs[0][0], 'Archaeopt')
self.assertEqual(seqs[-1][0], 'B.subtilis')
self.assertEqual(seqs[-1][-1], 'GGCAGCCAATCACGGCAGCC')
seqs = list(MinimalPhylipParser(self.noninterleaved_big))
self.assertEqual(len(seqs), 3)
self.assertEqual(seqs[0][0], 'Rhesus')
self.assertEqual(seqs[-1][0], 'Pig')
self.assertEqual(seqs[-1][1], 'tgtggcacagatactcatgccagctcgttacagcatgagaacagcagtttattactcactaaagacagaatgaatgtagaaaaggctgaattttgtaataaaagcaagcagcctgtcttagcaaagagccaacagagcagatgggctgaaagtaagggcacatgtaatgataggcagactcctaacacagagaaaaaggtagttctgaatactgatctcctgtatgggagaaacgaactgaataagcagaaacctgcgtgctctgacagtcctagagattcccaagatgttccttgg')
def test_empty(self):
"""MinimalFastaParser should return empty list from 'file' w/o labels"""
self.assertEqual(list(MinimalPhylipParser(self.empty)), [])