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src/b/i/biopython-HEAD/Bio/CodonAlign/CodonAlphabet.py   biopython(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC, Gapped, HasStopCodon, Alphabet, generic_dna
from Bio.Data.CodonTable import generic_by_id
 
class CodonAlphabet(Alphabet):
    """Generic Codon Alphabet with a size of three"""
    size = 3
    letters = None
    name = ''

src/b/i/biopython-HEAD/Bio/CodonAlign/CodonSeq.py   biopython(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC, Gapped, HasStopCodon, Alphabet
from Bio.Alphabet import generic_dna, _ungap
from Bio.Data.CodonTable import generic_by_id

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
 

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/SeqIO/__init__.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
 
from . import AbiIO

src/b/i/biopython-1.63/Bio/SeqIO/__init__.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
 
from . import AbiIO

src/b/i/biopython-HEAD/Bio/NeuralNetwork/Gene/Schema.py   biopython(Download)
class SchemaDNAAlphabet(Alphabet.Alphabet):
    """Alphabet of a simple Schema for DNA sequences.
 
    This defines a simple alphabet for DNA sequences that has a single
    character which can match any other character.

src/b/i/biopython-1.63/Bio/NeuralNetwork/Gene/Schema.py   biopython(Download)
class SchemaDNAAlphabet(Alphabet.Alphabet):
    """Alphabet of a simple Schema for DNA sequences.
 
    This defines a simple alphabet for DNA sequences that has a single
    character which can match any other character.

src/b/i/biopython-HEAD/Bio/SubsMat/__init__.py   biopython(Download)
                raise ValueError("Failed to store data in a dictionary")
        if alphabet is None:
            alphabet = Alphabet.Alphabet()
        assert Alphabet.generic_alphabet.contains(alphabet)
        self.alphabet = alphabet

src/b/i/biopython-HEAD/Bio/SubsMat/FreqTable.py   biopython(Download)
            raise ValueError("bad dict_type")
        if not alphabet:
            self.alphabet = Alphabet.Alphabet()
            self.alphabet.letters = self._alphabet_from_input()
 

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