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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
 
            alpha = Gapped(alpha, gap_char=gap)
        if stop:
            alpha = HasStopCodon(alpha, stop_symbol=stop)
    else:
        raise TypeError("Only Nuclteotide Alphabet is accepted!")

src/h/y/hy454-0.4.4/lib/hy454/_graph.py   hy454(Download)
from tempfile import mkstemp
 
from Bio.Alphabet import Gapped, HasStopCodon, _verify_alphabet
from Bio.Alphabet.IUPAC import (ambiguous_dna, ambiguous_rna,
        extended_protein, unambiguous_dna, unambiguous_rna)
_DNA_ALPHABET = Gapped(ambiguous_dna)
_RNA_ALPHABET = Gapped(ambiguous_rna)
_AMINO_ALPHABET = HasStopCodon(Gapped(extended_protein, gap_char=_GAP), stop_symbol=_STOP)
 
def _fix_ambigs(pwm, alphabet):
        })
        killchars += 'N'
    elif alphabet == _AMINO_ALPHABET:
        mapper.update({
            'B': 'DN',
 
    alph = None
    for _alph in (_DNA_ALPHABET, _RNA_ALPHABET, _AMINO_ALPHABET):
        for r in alignment:
            r.seq.alphabet = _alph

src/b/i/biopython-HEAD/Bio/Seq.py   biopython(Download)
                                 stop_symbol, to_stop, cds)
        if stop_symbol in protein:
            alphabet = Alphabet.HasStopCodon(codon_table.protein_alphabet,
                                             stop_symbol = stop_symbol)
        else:

src/b/i/biopython-1.63/Bio/Seq.py   biopython(Download)
                                 stop_symbol, to_stop, cds)
        if stop_symbol in protein:
            alphabet = Alphabet.HasStopCodon(codon_table.protein_alphabet,
                                             stop_symbol = stop_symbol)
        else:

src/b/i/biopython-HEAD/Bio/Align/AlignInfo.py   biopython(Download)
    print("Trying a protein sequence with gaps and stops")
 
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")

src/b/i/biopython-1.63/Bio/Align/AlignInfo.py   biopython(Download)
    print("Trying a protein sequence with gaps and stops")
 
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")

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/Tests/test_seq.py   biopython(Download)
           Seq.Seq("T.CGPK", Alphabet.Gapped(IUPAC.protein, ".")),
           Seq.Seq("T-CGPK", Alphabet.Gapped(IUPAC.protein, "-")),
           Seq.Seq("MEDG-KRXR*", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")),
           Seq.MutableSeq("ME-K-DRXR*XU", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")),
           Seq.Seq("MEDG-KRXR@", Alphabet.HasStopCodon(Alphabet.Gapped(IUPAC.extended_protein, "-"), "@")),
           Seq.Seq("ME-KR@", Alphabet.HasStopCodon(Alphabet.Gapped(IUPAC.protein, "-"), "@")),
           Seq.Seq("MEDG.KRXR@", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "@"), ".")),

src/b/i/biopython-1.63/Tests/test_seq.py   biopython(Download)
           Seq.Seq("T.CGPK", Alphabet.Gapped(IUPAC.protein, ".")),
           Seq.Seq("T-CGPK", Alphabet.Gapped(IUPAC.protein, "-")),
           Seq.Seq("MEDG-KRXR*", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")),
           Seq.MutableSeq("ME-K-DRXR*XU", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")),
           Seq.Seq("MEDG-KRXR@", Alphabet.HasStopCodon(Alphabet.Gapped(IUPAC.extended_protein, "-"), "@")),
           Seq.Seq("ME-KR@", Alphabet.HasStopCodon(Alphabet.Gapped(IUPAC.protein, "-"), "@")),
           Seq.Seq("MEDG.KRXR@", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "@"), ".")),