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src/c/o/cogent-1.5.3/cogent/app/infernal.py   cogent(Download)
from cogent.core.moltype import DNA, RNA
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
 
    #Get alignment in Stockholm format
    aln_file_string = stockholm_from_alignment(aln,GC_annotation=struct_dict)
 
    #get path to alignment filename

src/p/y/pycogent-HEAD/cogent/app/infernal.py   pycogent(Download)
from cogent.core.moltype import DNA, RNA
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
 
    #Get alignment in Stockholm format
    aln_file_string = stockholm_from_alignment(aln,GC_annotation=struct_dict)
 
    #get path to alignment filename

src/c/o/cogent-1.5.3/tests/test_app/test_infernal.py   cogent(Download)
from cogent.parse.rfam import MinimalRfamParser, ChangedRnaSequence, \
    ChangedSequence
from cogent.format.stockholm import stockholm_from_alignment
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
 
        self.struct2_aligned_dict = {'SS_cons':self.struct2_aligned_string}
 
        self.lines2 = stockholm_from_alignment(aln=self.seqs2_aligned,\
            GC_annotation=self.struct2_aligned_dict)
 

src/p/y/pycogent-HEAD/tests/test_app/test_infernal.py   pycogent(Download)
from cogent.parse.rfam import MinimalRfamParser, ChangedRnaSequence, \
    ChangedSequence
from cogent.format.stockholm import stockholm_from_alignment
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
 
        self.struct2_aligned_dict = {'SS_cons':self.struct2_aligned_string}
 
        self.lines2 = stockholm_from_alignment(aln=self.seqs2_aligned,\
            GC_annotation=self.struct2_aligned_dict)
 

src/p/y/pycogent-HEAD/tests/test_format/test_stockholm.py   pycogent(Download)
 #!/usr/bin/env python
"""Tests for Stockholm sequence format writer.
"""
from cogent.util.unit_test import TestCase, main
from cogent.format.stockholm import stockholm_from_alignment

src/c/o/cogent-1.5.3/tests/test_format/test_stockholm.py   cogent(Download)
 #!/usr/bin/env python
"""Tests for Stockholm sequence format writer.
"""
from cogent.util.unit_test import TestCase, main
from cogent.format.stockholm import stockholm_from_alignment