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src/b/i/biopython-HEAD/Bio/CodonAlign/__init__.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
 
from Bio.CodonAlign.CodonSeq import CodonSeq
from Bio.CodonAlign.CodonAlignment import CodonAlignment, mktest
from Bio.CodonAlign.CodonAlphabet import CodonAlphabet
                codon_seq += this_codon
                aa_num += 1
        return SeqRecord(CodonSeq(codon_seq, alphabet=alphabet), id=nucl.id)
    elif mode == 2:
        from collections import deque
                codon_seq += this_codon
                aa_num += 1
        return SeqRecord(CodonSeq(codon_seq, alphabet=alphabet,
                         rf_table=rf_table), id=nucl.id)
 
                            [v+int(gap_num) for v in full_rf_table[bp+1:]]
                    full_rf_table_lst[j] = full_rf_table
                    recs[j].seq = CodonSeq(seq,
                                           rf_table=recs[j].seq.rf_table,
                                           alphabet=recs[j].seq.alphabet)
                        [v+int(gap_num) for v in full_rf_table[bp:]]
                full_rf_table_lst[j] = full_rf_table
                recs[j].seq = CodonSeq(seq,
                                       rf_table=recs[j].seq.rf_table,
                                       alphabet=recs[j].seq.alphabet)

src/b/i/biopython-HEAD/Bio/CodonAlign/CodonAlignment.py   biopython(Download)
 
from Bio.CodonAlign.CodonAlphabet import default_codon_table, default_codon_alphabet
from Bio.CodonAlign.CodonSeq import _get_codon_list, CodonSeq, cal_dn_ds
from Bio.CodonAlign.chisq import chisqprob
 
        needed by CodonAlignment is met.
        """
        rec = [SeqRecord(CodonSeq(str(i.seq), alphabet=alphabet), id=i.id) \
                 for i in align._records]
        return cls(rec, alphabet=alphabet)