Python _create_terminal_gap_mask Examples

Example #1

File: test_mask.py Project: wasade/genome-sampler

    def test_create_terminal_gap_mask_one_chrome(self):
        obs = _create_terminal_gap_mask(self.msa1, self.mask5)
        npt.assert_array_equal(obs, [True, False, False, False])

        seqs = [
            skbio.DNA('ACG-', metadata=dict(id='s1')),
            skbio.DNA('AG-T', metadata=dict(id='s2')),
            skbio.DNA('-C-T', metadata=dict(id='s3'))]
        msa = skbio.TabularMSA(seqs, minter='id')
        obs = _create_terminal_gap_mask(msa, self.mask5)
        npt.assert_array_equal(obs, [True, False, False, False])

Example #2

File: test_mask.py Project: wasade/genome-sampler

    def test_create_terminal_gap_mask_all(self):
        seqs = [
            skbio.DNA('----', metadata=dict(id='s1')),
            skbio.DNA('AGAT', metadata=dict(id='s2')),
            skbio.DNA('----', metadata=dict(id='s3'))]
        msa = skbio.TabularMSA(seqs, minter='id')
        obs = _create_terminal_gap_mask(msa, self.mask2)
        npt.assert_array_equal(obs, [True, True, True, True])

        seqs = [
            skbio.DNA('ACG-', metadata=dict(id='s1')),
            skbio.DNA('AG-T', metadata=dict(id='s2')),
            skbio.DNA('----', metadata=dict(id='s3'))]
        msa = skbio.TabularMSA(seqs, minter='id')
        obs = _create_terminal_gap_mask(msa, self.mask5)
        npt.assert_array_equal(obs, [True, True, True, True])