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src/c/o/cogent-1.5.3/cogent/core/alignment.py   cogent(Download)
from cogent.core.sequence import frac_same, ModelSequence
from cogent.maths.stats.util import Freqs
from cogent.format.fasta import fasta_from_alignment
from cogent.format.phylip import phylip_from_alignment
from cogent.format.nexus import nexus_from_alignment
              returns a label str
        """
        return fasta_from_alignment(self, make_seqlabel=make_seqlabel)
 
    def toNexus(self, seq_type, interleave_len=50):

src/p/y/pycogent-HEAD/cogent/core/alignment.py   pycogent(Download)
from cogent.core.sequence import frac_same, ModelSequence
from cogent.maths.stats.util import Freqs
from cogent.format.fasta import fasta_from_alignment
from cogent.format.phylip import phylip_from_alignment
from cogent.format.nexus import nexus_from_alignment
              returns a label str
        """
        return fasta_from_alignment(self, make_seqlabel=make_seqlabel)
 
    def toNexus(self, seq_type, interleave_len=50):

src/c/o/cogent-1.5.3/cogent/format/motif.py   cogent(Download)
    align_subject_to_pdb, PYMOL_FUNCTION_STRING, MAIN_FUNCTION_STRING
from cogent.format.rna_struct import color_on_structure, draw_structure
from cogent.format.fasta import fasta_from_alignment
from cogent.core.moltype import PROTEIN, RNA, DNA
from cogent.core.alignment import Alignment,SequenceCollection
            write_dir+'/'+outfile_prefix+'_binding_site_alignment.fasta'
        out_file = open(out_path,'w')
        out_file.write(fasta_from_alignment(new_aln))
        out_file.close()
        print out_path

src/p/y/pycogent-HEAD/cogent/format/motif.py   pycogent(Download)
    align_subject_to_pdb, PYMOL_FUNCTION_STRING, MAIN_FUNCTION_STRING
from cogent.format.rna_struct import color_on_structure, draw_structure
from cogent.format.fasta import fasta_from_alignment
from cogent.core.moltype import PROTEIN, RNA, DNA
from cogent.core.alignment import Alignment,SequenceCollection
            write_dir+'/'+outfile_prefix+'_binding_site_alignment.fasta'
        out_file = open(out_path,'w')
        out_file.write(fasta_from_alignment(new_aln))
        out_file.close()
        print out_path

src/p/y/pycogent-HEAD/tests/test_format/test_fasta.py   pycogent(Download)
#!/usr/bin/env python
"""Tests for FASTA sequence format writer.
"""
from cogent.util.unit_test import TestCase, main
from cogent.format.fasta import fasta_from_sequences, fasta_from_alignment

src/c/o/cogent-1.5.3/tests/test_format/test_fasta.py   cogent(Download)
#!/usr/bin/env python
"""Tests for FASTA sequence format writer.
"""
from cogent.util.unit_test import TestCase, main
from cogent.format.fasta import fasta_from_sequences, fasta_from_alignment