Python distmat_muscle Examples

Example #1

File: pairwise_distances.py Project: sminot/deenurp

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))

Example #2

File: test_outliers.py Project: sminot/deenurp

 def setUpClass(cls):
     cls.taxa, cls.distmat = distmat_muscle(cls.fa,
                                            '{}_'.format(cls.tax_id))

Example #3

File: test_outliers.py Project: fhcrc/deenurp

 def setUpClass(cls):
     cls.taxa, cls.distmat = distmat_muscle(cls.fa, "{}_".format(cls.tax_id))