def test_mask2_wo_terminal_gap_mask(self):
obs = mask(self.msa1, self.mask2, "mask", False)
seqs = [
skbio.DNA('ACG', metadata=dict(id='s1')),
skbio.DNA('AG-', metadata=dict(id='s2')),
skbio.DNA('-C-', metadata=dict(id='s3'))]
exp = skbio.TabularMSA(seqs, minter='id')
self.assertEqual(obs, exp)
obs = mask(self.msa1, self.mask2, "caution", False)
seqs = [
skbio.DNA('AG', metadata=dict(id='s1')),
skbio.DNA('A-', metadata=dict(id='s2')),
skbio.DNA('--', metadata=dict(id='s3'))]
exp = skbio.TabularMSA(seqs, minter='id')
self.assertEqual(obs, exp)
def test_mask4_w_terminal_gap_mask(self):
obs = mask(self.msa2, self.mask4, "mask", True)
seqs = [
skbio.DNA('NNNGGTGCCA-CC--A', metadata=dict(id='s1')),
skbio.DNA('CTCGGTGCCA-CC--A', metadata=dict(id='s2')),
skbio.DNA('CTCGGTACCA-CC--A', metadata=dict(id='s3')),
skbio.DNA('CTCGGTGCCA-CCGGA', metadata=dict(id='S_4')),
skbio.DNA('CTCGGTGCCA-CC--A', metadata=dict(id='seq5.555')),
skbio.DNA('CTCGGTGCCA-CC--A', metadata=dict(id='s11'))]
exp = skbio.TabularMSA(seqs, minter='id')
self.assertEqual(obs, exp)
obs = mask(self.msa2, self.mask4, "caution", True)
seqs = [
skbio.DNA('NNNGGCCA-CC--A', metadata=dict(id='s1')),
skbio.DNA('CTCGGCCA-CC--A', metadata=dict(id='s2')),
skbio.DNA('CTCGGCCA-CC--A', metadata=dict(id='s3')),
skbio.DNA('CTCGGCCA-CCGGA', metadata=dict(id='S_4')),
skbio.DNA('CTCGGCCA-CC--A', metadata=dict(id='seq5.555')),
skbio.DNA('CTCGGCCA-CC--A', metadata=dict(id='s11'))]
exp = skbio.TabularMSA(seqs, minter='id')
self.assertEqual(obs, exp)