def test_make_otu_map_no_taxonomy(self): """make_otu_map should work without supplied taxonomy""" otu_to_seqid ={ '0':['ABC_0','DEF_1'], '1':['ABC_1'], 'x':['GHI_2', 'GHI_3','GHI_77'], 'z':['DEF_3','XYZ_1'] } obs = make_otu_map(otu_to_seqid) exp = """#Full OTU Counts #OTU ID\tABC\tDEF\tGHI\tXYZ 0\t1\t1\t0\t0 1\t1\t0\t0\t0 x\t0\t0\t3\t0 z\t0\t1\t0\t1""" self.assertEqual(obs, exp)
def test_make_otu_map_taxonomy(self): """make_otu_map should work with supplied taxonomy""" otu_to_seqid ={ '0':['ABC_0','DEF_1'], '1':['ABC_1'], 'x':['GHI_2', 'GHI_3','GHI_77'], 'z':['DEF_3','XYZ_1'] } taxonomy = {'0':'Bacteria;Firmicutes', 'x':'Bacteria;Bacteroidetes'} obs = make_otu_map(otu_to_seqid, taxonomy) exp = """#Full OTU Counts #OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage 0\t1\t1\t0\t0\tBacteria;Firmicutes 1\t1\t0\t0\t0\tNone x\t0\t0\t3\t0\tBacteria;Bacteroidetes z\t0\t1\t0\t1\tNone""" self.assertEqual(obs, exp)
def test_make_otu_map_no_taxonomy(self): """make_otu_map should work without supplied taxonomy""" otu_to_seqid = { '0': ['ABC_0', 'DEF_1'], '1': ['ABC_1'], 'x': ['GHI_2', 'GHI_3', 'GHI_77'], 'z': ['DEF_3', 'XYZ_1'] } obs = make_otu_map(otu_to_seqid) exp = """#Full OTU Counts #OTU ID\tABC\tDEF\tGHI\tXYZ 0\t1\t1\t0\t0 1\t1\t0\t0\t0 x\t0\t0\t3\t0 z\t0\t1\t0\t1""" self.assertEqual(obs, exp)
def test_make_otu_map_taxonomy(self): """make_otu_map should work with supplied taxonomy""" otu_to_seqid = { '0': ['ABC_0', 'DEF_1'], '1': ['ABC_1'], 'x': ['GHI_2', 'GHI_3', 'GHI_77'], 'z': ['DEF_3', 'XYZ_1'] } taxonomy = {'0': 'Bacteria;Firmicutes', 'x': 'Bacteria;Bacteroidetes'} obs = make_otu_map(otu_to_seqid, taxonomy) exp = """#Full OTU Counts #OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage 0\t1\t1\t0\t0\tBacteria;Firmicutes 1\t1\t0\t0\t0\tNone x\t0\t0\t3\t0\tBacteria;Bacteroidetes z\t0\t1\t0\t1\tNone""" self.assertEqual(obs, exp)