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src/c/o/cogent-1.5.3/tests/test_app/test_clustalw.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.clustalw import Clustalw, alignUnalignedSeqsFromFile,\
    alignUnalignedSeqs, alignTwoAlignments, addSeqsToAlignment,\
    buildTreeFromAlignment, build_tree_from_alignment, \
    def test_build_tree_from_alignment(self):
        """Clustalw should return a tree built from the passed alignment"""
        tree_short = build_tree_from_alignment(self.build_tree_seqs_short, \
                RNA, best_tree=False)
        num_seqs = flatten(self.build_tree_seqs_short).count('>')
        self.assertEqual(len(tree_short.tips()), num_seqs)
 
        tree_long = build_tree_from_alignment(self.build_tree_seqs_long, \
                self.fail()
 
        tree_short = build_tree_from_alignment(self.build_tree_seqs_short, \
                RNA, best_tree=True, params={'-bootstrap':3})
        num_seqs = flatten(self.build_tree_seqs_short).count('>')

src/p/y/pycogent-HEAD/tests/test_app/test_clustalw.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.clustalw import Clustalw, alignUnalignedSeqsFromFile,\
    alignUnalignedSeqs, alignTwoAlignments, addSeqsToAlignment,\
    buildTreeFromAlignment, build_tree_from_alignment, \
    def test_build_tree_from_alignment(self):
        """Clustalw should return a tree built from the passed alignment"""
        tree_short = build_tree_from_alignment(self.build_tree_seqs_short, \
                RNA, best_tree=False)
        num_seqs = flatten(self.build_tree_seqs_short).count('>')
        self.assertEqual(len(tree_short.tips()), num_seqs)
 
        tree_long = build_tree_from_alignment(self.build_tree_seqs_long, \
                self.fail()
 
        tree_short = build_tree_from_alignment(self.build_tree_seqs_short, \
                RNA, best_tree=True, params={'-bootstrap':3})
        num_seqs = flatten(self.build_tree_seqs_short).count('>')