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src/c/o/cogent-1.5.3/cogent/parse/cmfinder.py   cogent(Download)
#!/usr/bin/env python
 
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import wuss_to_vienna, Pairs
from cogent.parse.rfam     import RfamParser
    """
    for info, alignment, struct in RfamParser(lines,strict=False):
        struct = wuss_to_vienna(struct)
        pairs = struct.toPairs()
    return [alignment, pairs]

src/p/y/pycogent-HEAD/cogent/parse/cmfinder.py   pycogent(Download)
#!/usr/bin/env python
 
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import wuss_to_vienna, Pairs
from cogent.parse.rfam     import RfamParser
    """
    for info, alignment, struct in RfamParser(lines,strict=False):
        struct = wuss_to_vienna(struct)
        pairs = struct.toPairs()
    return [alignment, pairs]

src/c/o/cogent-1.5.3/cogent/parse/cove.py   cogent(Download)
#!/usr/bin/env python
 
from string                import split,strip
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna

src/c/o/cogent-1.5.3/cogent/parse/consan.py   cogent(Download)
#!/usr/bin/env python
 
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna
from cogent.util.transform import make_trans
 

src/c/o/cogent-1.5.3/cogent/app/infernal.py   cogent(Download)
from cogent.core.alignment import SequenceCollection, Alignment, DataError
from cogent.format.stockholm import stockholm_from_alignment
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
from os import remove
 

src/p/y/pycogent-HEAD/cogent/parse/cove.py   pycogent(Download)
#!/usr/bin/env python
 
from string                import split,strip
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna

src/p/y/pycogent-HEAD/cogent/parse/consan.py   pycogent(Download)
#!/usr/bin/env python
 
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna
from cogent.util.transform import make_trans
 

src/p/y/pycogent-HEAD/cogent/app/infernal.py   pycogent(Download)
from cogent.core.alignment import SequenceCollection, Alignment, DataError
from cogent.format.stockholm import stockholm_from_alignment
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
from os import remove
 

src/c/o/cogent-1.5.3/tests/test_app/test_infernal.py   cogent(Download)
    ChangedSequence
from cogent.format.stockholm import stockholm_from_alignment
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
 
__author__ = "Jeremy Widmann"
        self.assertEqual(aln.todict(),self.seqs1_aligned)
        #Check correct struct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_aligned_struct_string)
 
        self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
        #structure should be correct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_and_seqs2_aligned_struct_string)
 
        self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
        #structure should be correct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_and_seqs2_aligned_struct_string)
 
        self.assertEqual(aln.todict(),self.seqs1_aligned)
        #Check correct struct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_aligned_struct_string)
 

src/p/y/pycogent-HEAD/tests/test_app/test_infernal.py   pycogent(Download)
    ChangedSequence
from cogent.format.stockholm import stockholm_from_alignment
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
 
__author__ = "Jeremy Widmann"
        self.assertEqual(aln.todict(),self.seqs1_aligned)
        #Check correct struct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_aligned_struct_string)
 
        self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
        #structure should be correct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_and_seqs2_aligned_struct_string)
 
        self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
        #structure should be correct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_and_seqs2_aligned_struct_string)
 
        self.assertEqual(aln.todict(),self.seqs1_aligned)
        #Check correct struct
        self.assertEqual(wuss_to_vienna(str(struct)),\
            self.seqs1_aligned_struct_string)
 

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