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')