def action(args):
pfx = splitext(basename(args.seqs))[0]
if args.aligner == 'vsearch':
taxa, distmat = filter_outliers.distmat_pairwise(
args.seqs, pfx, args.aligner, iddef=args.iddef, threads=args.threads)
elif args.aligner == 'cmalign':
taxa, distmat = filter_outliers.distmat_cmalign(args.seqs, pfx, cpu=args.threads)
elif args.aligner == 'muscle':
taxa, distmat = filter_outliers.distmat_muscle(args.seqs, pfx)
if args.distmat:
numpy.savetxt(args.distmat, distmat, delimiter=',', header=','.join(taxa))
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 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))
