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 )
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 )
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 )
def test_snps_taxon4_exc2(): gene_syn = GeneSNP() with pytest.raises(FilterFails): filter_genesyn_by_taxon_id( gene_syn, filter_list=None )
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 )