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src/b/i/biopython---popgen-HEAD/src/PopGen/Gio/fastPhaseOutputIO.py   biopython---popgen(Download)
import re 
import logging
from Bio.Align.Generic import Alignment
from Bio.Alphabet import single_letter_alphabet
 
        alphabet = single_letter_alphabet
 
    align = Alignment(alphabet)
    records = align._records    # hack to append SeqRecord objects to Alignment
                                # see bugs 2553/2554

src/b/i/biopython-1.63/Bio/FSSP/FSSPTools.py   biopython(Download)
class FSSPAlign(Generic.Alignment):
    def _add_numbering_table(self, new_record):
        new_record.annotations['abs2pdb'] = {}
        new_record.annotations['pdb2abs'] = {}
 
            # loop within a position
            mult_align_dict[j] += align_dict.abs(i).pos_align_dict[j].aa
    fssp_align = Generic.Alignment(Alphabet.Gapped(
                                   Alphabet.IUPAC.extended_protein))
    for i in sorted(mult_align_dict):

src/b/i/biopython-1.63/Bio/Align/AlignInfo.py   biopython(Download)
    print("Quick test")
    from Bio import AlignIO
    from Bio.Align.Generic import Alignment
 
    filename = "../../Tests/GFF/multi.fna"
 
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")
    a.add_sequence("ID002", "MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*")

src/b/i/biopython-HEAD/Bio/Align/AlignInfo.py   biopython(Download)
    print("Quick test")
    from Bio import AlignIO
    from Bio.Align.Generic import Alignment
 
    filename = "../../Tests/GFF/multi.fna"
 
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")
    a.add_sequence("ID002", "MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*")

src/b/i/biopython---popgen-HEAD/src/PopGen/Gio/HaplotypesGenerator.py   biopython---popgen(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align.Generic import Alignment
#from PopGen.Exceptions import NotImplementedError
 
 
        """
        alignment = Alignment(self.alphabet)
 
        # initialize random generator

src/b/i/biopython-1.63/Bio/Blast/Record.py   biopython(Download)
                n += 1
 
        generic = Generic.Alignment(alphabet)
        for (name, seq) in zip(seq_names, seq_parts):
            generic.add_sequence(name, seq)

src/b/i/biopython-1.63/Bio/Align/__init__.py   biopython(Download)
 
#We only import this and subclass it for some limited backward compatibility.
from Bio.Align.Generic import Alignment as _Alignment
 
 
class MultipleSeqAlignment(_Alignment):

src/b/i/biopython-HEAD/Bio/Align/__init__.py   biopython(Download)
 
#We only import this and subclass it for some limited backward compatibility.
from Bio.Align.Generic import Alignment as _Alignment
 
 
class MultipleSeqAlignment(_Alignment):

src/b/i/biopython-1.63/Bio/AlignIO/__init__.py   biopython(Download)
 
from Bio.Align import MultipleSeqAlignment
from Bio.Align.Generic import Alignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
from Bio.File import as_handle

src/b/i/biopython-HEAD/Bio/AlignIO/__init__.py   biopython(Download)
 
from Bio.Align import MultipleSeqAlignment
from Bio.Align.Generic import Alignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
from Bio.File import as_handle

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