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))