def test_align_no_blank_columns(self):
"""correctly handle a file with no white space at line starts"""
parser = MinimalNexusAlignParser("data/nexus_aa.nxs")
seqs = {n: s for n, s in parser}
self.assertEqual(len(seqs), 10) # 10 taxa
lengths = set(len(seqs[n]) for n in seqs)
self.assertEqual(lengths, {234}) # all same length and equal 234
def test_align_with_spaced_seqs(self):
"""correctly handle an alignment block with spaces in seqs"""
parser = MinimalNexusAlignParser("data/nexus_dna.nex")
seqs = {n: s for n, s in parser}
self.assertEqual(len(seqs), 10) # 10 taxa
lengths = set(len(seqs[n]) for n in seqs)
self.assertEqual(lengths, {705}) # all same length and equal 705
def test_align_from_mixed(self):
"""correctly handle a file with tree and alignment block"""
parser = MinimalNexusAlignParser("data/nexus_mixed.nex")
got = {n: s for n, s in parser}
expect = {
"fish": "ACATAGAGGGTACCTCTAAG",
"frog": "ACATAGAGGGTACCTCTAAG",
"snake": "ACATAGAGGGTACCTCTAAG",
"mouse": "ACATAGAGGGTACCTCTAAG",
}
self.assertEqual(got, expect)
def test_align_with_comments(self):
"""correctly handle an alignment block containing comments"""
parser = MinimalNexusAlignParser("data/nexus_comments.nex")
got = {n: s for n, s in parser}
expect = {
"Ephedra": "TTAAGCCATGCATGTCTAAGTATGAACTAATTCCAAACGGTGA",
"Gnetum": "TTAAGCCATGCATGTCTATGTACGAACTAATC-AGAACGGTGA",
"Welwitschia": "TTAAGCCATGCACGTGTAAGTATGAACTAGTC-GAAACGGTGA",
"Ginkgo": "TTAAGCCATGCATGTGTAAGTATGAACTCTTTACAGACTGTGA",
"Pinus": "TTAAGCCATGCATGTCTAAGTATGAACTAATTGCAGACTGTGA",
}
self.assertEqual(got, expect)