Python blast_lca Examples

Programming Language: Python

Namespace/Package Name: metagenomics

Method/Function: blast_lca

Examples at hotexamples.com: 2

Python blast_lca - 2 examples found. These are the top rated real world Python examples of metagenomics.blast_lca extracted from open source projects. You can rate examples to help us improve the quality of examples.

Example #1

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def test_blast_lca(taxa_db_simple, simple_m8):
    test_path = join(util.file.get_test_input_path(), 'TestTaxonomy')
    expected = textwrap.dedent("""\
    C\tM04004:13:000000000-AGV3H:1:1101:12068:2105\t2
    C\tM04004:13:000000000-AGV3H:1:1101:13451:2146\t2
    C\tM04004:13:000000000-AGV3H:1:1101:13509:2113\t2
    C\tM04004:13:000000000-AGV3H:1:1101:14644:2160\t2
    C\tM04004:13:000000000-AGV3H:1:1101:18179:2130\t2
    C\tM04004:13:000000000-AGV3H:1:1111:10629:2610\t2
    C\tM04004:13:000000000-AGV3H:1:1111:10629:26101\t2
    """)
    out = StringIO()
    with simple_m8 as f:
        metagenomics.blast_lca(taxa_db_simple, f, out, paired=True)
        out.seek(0)
        assert out.read() == expected

Example #2

Show file

File: test_metagenomics.py Project: tianyabeef/viral-ngs

def test_blast_lca(taxa_db_simple, simple_m8):
    test_path = join(util.file.get_test_input_path(),
                             'TestTaxonomy')
    expected = textwrap.dedent("""\
    M04004:13:000000000-AGV3H:1:1101:12068:2105\t2
    M04004:13:000000000-AGV3H:1:1101:13451:2146\t2
    M04004:13:000000000-AGV3H:1:1101:13509:2113\t2
    M04004:13:000000000-AGV3H:1:1101:14644:2160\t2
    M04004:13:000000000-AGV3H:1:1101:18179:2130\t2
    M04004:13:000000000-AGV3H:1:1111:10629:2610\t2
    M04004:13:000000000-AGV3H:1:1111:10629:26101\t2
    """)
    out = StringIO()
    with simple_m8 as f:
        metagenomics.blast_lca(taxa_db_simple, f, out, paired=True)
        out.seek(0)
        assert out.read() == expected