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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)
        for r in alignment:
            r.seq.alphabet = _alph
        if all([_verify_alphabet(r.seq.upper()) for r in alignment]):
            alph = _alph
            break

src/b/i/biopython-1.63/Bio/NeuralNetwork/Gene/Signature.py   biopython(Download)
"""
# biopython
from Bio.Alphabet import _verify_alphabet
from Bio.Seq import Seq
 
                        first_seq = Seq(first_sig, alphabet)
                        second_seq = Seq(second_sig, alphabet)
                        if _verify_alphabet(first_seq) \
                        and _verify_alphabet(second_seq):
                            all_sigs = self._add_sig(all_sigs,

src/b/i/biopython-HEAD/Bio/NeuralNetwork/Gene/Signature.py   biopython(Download)
"""
# biopython
from Bio.Alphabet import _verify_alphabet
from Bio.Seq import Seq
 
                        first_seq = Seq(first_sig, alphabet)
                        second_seq = Seq(second_sig, alphabet)
                        if _verify_alphabet(first_seq) \
                        and _verify_alphabet(second_seq):
                            all_sigs = self._add_sig(all_sigs,

src/g/i/giraffe-2.0/src/giraffe/features.py   giraffe(Download)
from Bio.Alphabet import IUPAC, _verify_alphabet
from Bio.Seq import Seq
import re
import os
 
    if alphabet is None:
      alphabet = IUPAC.unambiguous_dna
    if not _verify_alphabet(Seq(sequence.upper(), alphabet)):
      raise Exception("Sequence %s contains illegal character. Expecting %s only." % (sequence, alphabet.letters))
  return sequence

src/b/i/biopython-1.63/Bio/NeuralNetwork/Gene/Pattern.py   biopython(Download)
 
# biopython
from Bio.Alphabet import _verify_alphabet
from Bio.Seq import Seq, MutableSeq
 
                for pattern_item in test_pattern:
                    pattern_seq = Seq(pattern_item, self._alphabet)
                    if not(_verify_alphabet(pattern_seq)):
                        raise ValueError("Pattern %s not matching alphabet %s"
                                         % (cur_pattern, self._alphabet))

src/b/i/biopython-1.63/Bio/NeuralNetwork/Gene/Motif.py   biopython(Download)
"""
# biopython
from Bio.Alphabet import _verify_alphabet
from Bio.Seq import Seq
 
                if alphabet is not None:
                    motif_seq = Seq(motif, alphabet)
                    if _verify_alphabet(motif_seq):
                        all_motifs = self._add_motif(all_motifs, motif)
 

src/b/i/biopython-HEAD/Bio/NeuralNetwork/Gene/Pattern.py   biopython(Download)
 
# biopython
from Bio.Alphabet import _verify_alphabet
from Bio.Seq import Seq, MutableSeq
 
                for pattern_item in test_pattern:
                    pattern_seq = Seq(pattern_item, self._alphabet)
                    if not(_verify_alphabet(pattern_seq)):
                        raise ValueError("Pattern %s not matching alphabet %s"
                                         % (cur_pattern, self._alphabet))

src/b/i/biopython-HEAD/Bio/NeuralNetwork/Gene/Motif.py   biopython(Download)
"""
# biopython
from Bio.Alphabet import _verify_alphabet
from Bio.Seq import Seq
 
                if alphabet is not None:
                    motif_seq = Seq(motif, alphabet)
                    if _verify_alphabet(motif_seq):
                        all_motifs = self._add_motif(all_motifs, motif)