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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_aln_tree_seqs(self):
        "aln_tree_seqs returns the muscle alignment and tree from iteration2"
        tree, aln = aln_tree_seqs(path.join(self.temp_dir, 'seq1.txt'), 
                                   tree_type="neighborjoining",
                                   WorkingDir=self.temp_dir,
        except OSError:
            pass
        tree, aln = aln_tree_seqs(path.join(self.temp_dir_spaces,\
                                    'muscle_test_seq1.txt'), 
                                    tree_type="neighborjoining",

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_aln_tree_seqs(self):
        "aln_tree_seqs returns the muscle alignment and tree from iteration2"
        tree, aln = aln_tree_seqs(path.join(self.temp_dir, 'seq1.txt'), 
                                   tree_type="neighborjoining",
                                   WorkingDir=self.temp_dir,
        except OSError:
            pass
        tree, aln = aln_tree_seqs(path.join(self.temp_dir_spaces,\
                                    'muscle_test_seq1.txt'), 
                                    tree_type="neighborjoining",