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src/p/y/pynast-1.2.2/pynast/util.py   pynast(Download)
from cogent.app.muscle_v38 import align_unaligned_seqs as muscle_align_unaligned_seqs
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.app.clustalw import align_unaligned_seqs as clustal_align_unaligned_seqs
from cogent.parse.blast import BlastResult
from cogent.parse.fasta import MinimalFastaParser

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_align_unaligned_seqs(self):
        """Clustalw align_unaligned_seqs should work as expected"""
        res = align_unaligned_seqs(self.seqs1, RNA)
        self.assertEqual(res.toFasta(), self.aln1_fasta)
 

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_align_unaligned_seqs(self):
        """Clustalw align_unaligned_seqs should work as expected"""
        res = align_unaligned_seqs(self.seqs1, RNA)
        self.assertEqual(res.toFasta(), self.aln1_fasta)
 

src/p/y/pynast-1.2.2/tests/test_util.py   pynast(Download)
from cogent.app.muscle_v38 import align_unaligned_seqs as muscle_align_unaligned_seqs
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.app.clustalw import align_unaligned_seqs as clustal_align_unaligned_seqs
from cogent.parse.fasta import MinimalFastaParser
from cogent.util.unit_test import TestCase, main