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src/c/o/cogent-1.5.3/tests/test_app/test_muscle_v38.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.muscle_v38 import Muscle, muscle_seqs, aln_tree_seqs, \
        align_unaligned_seqs, build_tree_from_alignment, \
        align_and_build_tree, add_seqs_to_alignment, align_two_alignments
    def test_build_tree_from_alignment(self):
        """Muscle should return a tree built from the passed alignment"""
        tree_short = build_tree_from_alignment(build_tree_seqs_short, DNA)
        num_seqs = flatten(build_tree_seqs_short).count('>')
        self.assertEqual(len(tree_short.tips()), num_seqs)
 
        tree_long = build_tree_from_alignment(build_tree_seqs_long, DNA)

src/p/y/pycogent-HEAD/tests/test_app/test_muscle_v38.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.muscle_v38 import Muscle, muscle_seqs, aln_tree_seqs, \
        align_unaligned_seqs, build_tree_from_alignment, \
        align_and_build_tree, add_seqs_to_alignment, align_two_alignments
    def test_build_tree_from_alignment(self):
        """Muscle should return a tree built from the passed alignment"""
        tree_short = build_tree_from_alignment(build_tree_seqs_short, DNA)
        num_seqs = flatten(build_tree_seqs_short).count('>')
        self.assertEqual(len(tree_short.tips()), num_seqs)
 
        tree_long = build_tree_from_alignment(build_tree_seqs_long, DNA)