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)
