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src/b/i/biopython-HEAD/Bio/Seq.py   biopython(Download)
        if str(sequence[:3]).upper() not in table.start_codons:
            raise CodonTable.TranslationError(
                "First codon '%s' is not a start codon" % sequence[:3])
        if n % 3 != 0:
            raise CodonTable.TranslationError(
                "Sequence length %i is not a multiple of three" % n) 
        if str(sequence[-3:]).upper() not in stop_codons:
            raise CodonTable.TranslationError(
                "Final codon '%s' is not a stop codon" % sequence[-3:])
                if cds:
                    raise CodonTable.TranslationError(
                        "Extra in frame stop codon found.")
                if to_stop:
                    break
            else:
                raise CodonTable.TranslationError(
                    "Codon '%s' is invalid" % codon)
    return "".join(amino_acids)
 

src/b/i/biopython-1.63/Bio/Seq.py   biopython(Download)
        if str(sequence[:3]).upper() not in table.start_codons:
            raise CodonTable.TranslationError(
                "First codon '%s' is not a start codon" % sequence[:3])
        if n % 3 != 0:
            raise CodonTable.TranslationError(
                "Sequence length %i is not a multiple of three" % n) 
        if str(sequence[-3:]).upper() not in stop_codons:
            raise CodonTable.TranslationError(
                "Final codon '%s' is not a stop codon" % sequence[-3:])
                if cds:
                    raise CodonTable.TranslationError(
                        "Extra in frame stop codon found.")
                if to_stop:
                    break
            else:
                raise CodonTable.TranslationError(
                    "Codon '%s' is invalid" % codon)
    return "".join(amino_acids)
 

src/b/i/biopython-HEAD/Tests/test_Seq_objs.py   biopython(Download)
from Bio.Data.IUPACData import ambiguous_dna_values, ambiguous_rna_values
from Bio.Seq import Seq, UnknownSeq, MutableSeq, translate
from Bio.Data.CodonTable import TranslationError, CodonTable
 
#This is just the standard table with less stop codons

src/b/i/biopython-HEAD/Tests/test_SeqIO_features.py   biopython(Download)
from Bio.Alphabet import generic_dna, generic_rna, generic_protein
from Bio import SeqIO
from Bio.Data.CodonTable import TranslationError
from Bio.Seq import Seq, UnknownSeq, MutableSeq, reverse_complement
from Bio.SeqRecord import SeqRecord

src/b/i/biopython-HEAD/Tests/test_seq.py   biopython(Download)
from Bio.Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
from Bio.Data.IUPACData import ambiguous_dna_values, ambiguous_rna_values
from Bio.Data.CodonTable import TranslationError
 
 

src/b/i/biopython-HEAD/Tests/test_CodonTable.py   biopython(Download)
from Bio.Data.CodonTable import ambiguous_rna_by_id, ambiguous_dna_by_id
from Bio.Data.CodonTable import unambiguous_rna_by_id
from Bio.Data.CodonTable import list_ambiguous_codons, TranslationError
 
#Check the extension of stop codons to include well defined ambiguous ones

src/b/i/biopython-1.63/Tests/test_Seq_objs.py   biopython(Download)
from Bio.Data.IUPACData import ambiguous_dna_values, ambiguous_rna_values
from Bio.Seq import Seq, UnknownSeq, MutableSeq, translate
from Bio.Data.CodonTable import TranslationError, CodonTable
 
#This is just the standard table with less stop codons

src/b/i/biopython-1.63/Tests/test_SeqIO_features.py   biopython(Download)
from Bio.Alphabet import generic_dna, generic_rna, generic_protein
from Bio import SeqIO
from Bio.Data.CodonTable import TranslationError
from Bio.Seq import Seq, UnknownSeq, MutableSeq, reverse_complement
from Bio.SeqRecord import SeqRecord

src/b/i/biopython-1.63/Tests/test_seq.py   biopython(Download)
from Bio.Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
from Bio.Data.IUPACData import ambiguous_dna_values, ambiguous_rna_values
from Bio.Data.CodonTable import TranslationError
 
 

src/b/i/biopython-1.63/Tests/test_CodonTable.py   biopython(Download)
from Bio.Data.CodonTable import ambiguous_rna_by_id, ambiguous_dna_by_id
from Bio.Data.CodonTable import unambiguous_rna_by_id
from Bio.Data.CodonTable import list_ambiguous_codons, TranslationError
 
#Check the extension of stop codons to include well defined ambiguous ones