Ejemplo n.º 1
0
def test_snps_taxon2_rev(ncbi_taxonomy):
    # will find it
    filter_list = [
        taxon.taxon_id
        for taxon in ncbi_taxonomy
        if 'clostridium' in taxon.s_name
    ]
    taxon_id = ncbi_taxonomy.find_by_name('methanobrevibacter')[0]
    gene_syn = GeneSNP(taxon_id=taxon_id)

    assert filter_genesyn_by_taxon_id(
        gene_syn,
        ncbi_taxonomy,
        filter_list=filter_list,
        exclude=True
    )
Ejemplo n.º 2
0
def test_snps_taxon3(ncbi_taxonomy):
    # will find it
    filter_list = [
        taxon.taxon_id
        for taxon in ncbi_taxonomy
        if 'clostridium' in taxon.s_name
    ]
    taxon_id = ncbi_taxonomy.find_by_name('methanobrevibacter')[0]
    gene_syn = GeneSNP(taxon_id=taxon_id)

    assert not filter_genesyn_by_taxon_id(
        gene_syn,
        ncbi_taxonomy,
        filter_list=filter_list,
        exclude=False,
        func=mgkit.taxon.is_ancestor
    )
Ejemplo n.º 3
0
def test_snps_taxon1(ncbi_taxonomy):
    # will find it
    filter_list = [
        taxon.taxon_id
        for taxon in ncbi_taxonomy
        if 'methanobrevibacter' in taxon.s_name.lower()
    ]
    taxon_id = ncbi_taxonomy.find_by_name('methanobrevibacter')[0]
    gene_syn = GeneSNP(taxon_id=taxon_id)


    assert filter_genesyn_by_taxon_id(
        gene_syn,
        ncbi_taxonomy,
        filter_list=filter_list,
        exclude=False
    )
Ejemplo n.º 4
0
def test_snps_taxon4_exc2():
    gene_syn = GeneSNP()
    with pytest.raises(FilterFails):
        filter_genesyn_by_taxon_id(
            gene_syn, filter_list=None
        )
Ejemplo n.º 5
0
def test_snps_taxon4_exc1():
    gene_syn = GeneSNP()
    with pytest.raises(FilterFails):
        filter_genesyn_by_taxon_id(
            gene_syn, filter_list=range(10), taxonomy=None, func=filter
        )