def test_condense_ids_rank(self):
with open(M8_FILE) as m8f, open(FASTA_FILE) as faf:
tbl = assign_contigs(m8f, genfile=GENBANK_ABBREV, seqfile=faf)
tbl = compress_assigned_contigs(tbl, rank='phylum', min_cov=0, max_cov=10)
self.assertEqual(tbl.shape[0], 2)
def test_contig_assignment_with_fasta(self):
with open(M8_FILE) as m8f, open(FASTA_FILE) as faf:
tbl = assign_contigs(m8f, genfile=GENBANK_ABBREV, seqfile=faf)
self.assertEqual(tbl.shape[0], 3)
self.assertEqual(tbl.shape[1], 6)
def test_condense_ids_wta(self):
with open(M8_FILE) as m8f, open(FASTA_FILE) as faf:
tbl = assign_contigs(m8f, genfile=GENBANK_ABBREV, seqfile=faf)
tbl = compress_assigned_contigs(tbl, min_cov=0, max_cov=10)
tbl = condense_winner_takes_all(tbl)
self.assertEqual(tbl.shape[0], 3)
def test_contig_assignment(self):
with open(M8_FILE) as m8f:
tbl = assign_contigs(m8f, genfile=GENBANK_ABBREV)
self.assertEqual(tbl.shape[0], 3)
self.assertEqual(tbl.shape[1], 4)