def test_parse_usearch_allpairs(self):
filename = util.data_path('e_faecalis.head.allpairs')
with open(util.data_path('e_faecalis.head.fasta')) as f:
seqs = SeqIO.parse(f, 'fasta')
seqnames = [seq.id for seq in seqs]
distmat = filter_outliers.parse_usearch_allpairs(filename, seqnames)
self.assertEqual(len(seqnames), distmat.shape[0])
def test_parse_usearch_allpairs(self):
filename = util.data_path("e_faecalis.head.allpairs")
with open(util.data_path("e_faecalis.head.fasta")) as f:
seqs = SeqIO.parse(f, "fasta")
seqnames = [seq.id for seq in seqs]
distmat = filter_outliers.parse_usearch_allpairs(filename, seqnames)
self.assertEqual(len(seqnames), distmat.shape[0])
def test_distmat_pairwise_vsearch(self):
infile = util.data_path("e_faecalis.head.fasta")
taxa, distmat = filter_outliers.distmat_pairwise(infile, "foo", "vsearch", wrap.VSEARCH)
self.assertEqual(distmat.shape[0], len(taxa))
def setUp(self):
self.sequences = SeqIO.parse(
util.data_path('taxon171552.seqs.fasta'), 'fasta')
def setUp(self):
self.sequences = list(SeqIO.parse(util.data_path('test_input.fasta'), 'fasta'))
def setUp(self):
self.infile = util.data_path('fusobacterium_nucleatum_refs.uc')
def test_distmat_pairwise_vsearch(self):
infile = util.data_path('e_faecalis.head.fasta')
taxa, distmat = filter_outliers.distmat_pairwise(
infile, 'foo', 'vsearch', wrap.VSEARCH)
self.assertEqual(distmat.shape[0], len(taxa))
def setUp(self):
self.sequencefile = util.data_path('test_input.fasta')
