Logo Search packages:      
Sourcecode: python-biopython version File versions

Translate.py

import string
from Bio import Alphabet, Seq
from Bio.Data import CodonTable

class Translator:
    def __init__(self, table):
        self.table = table
        self._encoded = {}

    def translate(self, seq, stop_symbol = "*"):
        assert seq.alphabet == self.table.nucleotide_alphabet, \
               "cannot translate from the given alphabet (%s)" % seq.alphabet
        s = seq.data
        letters = []
        append = letters.append
        table = self.table
        get = table.forward_table.get
        n = len(seq)
        for i in range(0, n-n%3, 3):
            append(get(s[i:i+3], stop_symbol))

        # return with the correct alphabet encoding (cache the encoding)
        try:
            alphabet = self._encoded[stop_symbol]
        except KeyError:
            alphabet = Alphabet.HasStopCodon(table.protein_alphabet)
            self._encoded[stop_symbol] = alphabet

        return Seq.Seq(string.join(letters, ""), alphabet)
                           
    def translate_to_stop(self, seq):
        # This doesn't have a stop encoding
        assert seq.alphabet == self.table.nucleotide_alphabet, \
               "cannot translate from given alphabet (have %s, need %s)" %\
               (seq.alphabet, self.table.nucleotide_alphabet)
        s = seq.data
        letters = []
        append = letters.append
        table = self.table.forward_table
        n = len(seq)
        try:
            for i in range(0, n-n%3, 3):
                append(table[s[i:i+3]])
        except KeyError:
            # Stop at the first codon failure
            pass
        return Seq.Seq(string.join(letters, ""), self.table.protein_alphabet)

    def back_translate(self, seq):
        # includes the stop codon
        if not isinstance(seq.alphabet, Alphabet.HasStopCodon):
            return self._back_translate_no_stop(seq)
        assert seq.alphabet.alphabet == self.table.protein_alphabet, \
               "cannot back translate from the given alphabet (%s)" % \
               seq.alphabet.alphabet
        s = seq.data
        letter = seq.alphabet.stop_symbol
        letters = []
        append = letters.append
        table = self.table.back_table
        for c in seq.data:
            if c == letter:
                append(table[None])
            else:
                append(table[c])
        return Seq.Seq(string.join(letters, ""),
                       self.table.nucleotide_alphabet)

    def _back_translate_no_stop(self, seq):
        # does not allow a stop codon
        assert seq.alphabet == self.table.protein_alphabet, \
               "cannot back translate from the given alphabet (%s)" % \
               seq.alphabet
        s = seq.data
        letters = []
        append = letters.append
        table = self.table.back_table
        for c in seq.data:
            append(table[c])
        return Seq.Seq(string.join(letters, ""),
                       self.table.nucleotide_alphabet)

unambiguous_dna_by_name = {}
for key, value in CodonTable.unambiguous_dna_by_name.items():
    unambiguous_dna_by_name[key] = Translator(value)
unambiguous_dna_by_id = {}
for key, value in CodonTable.unambiguous_dna_by_id.items():
    unambiguous_dna_by_id[key] = Translator(value)

unambiguous_rna_by_name = {}
for key, value in CodonTable.unambiguous_rna_by_name.items():
    unambiguous_rna_by_name[key] = Translator(value)
unambiguous_rna_by_id = {}
for key, value in CodonTable.unambiguous_rna_by_id.items():
    unambiguous_rna_by_id[key] = Translator(value)

# XXX Ambiguous - can be done the same except for stop codons!
ambiguous_dna_by_name = {}
for key, value in CodonTable.ambiguous_dna_by_name.items():
    ambiguous_dna_by_name[key] = Translator(value)
ambiguous_dna_by_id = {}
for key, value in CodonTable.ambiguous_dna_by_id.items():
    ambiguous_dna_by_id[key] = Translator(value)

ambiguous_rna_by_name = {}
for key, value in CodonTable.ambiguous_rna_by_name.items():
    ambiguous_rna_by_name[key] = Translator(value)
ambiguous_rna_by_id = {}
for key, value in CodonTable.ambiguous_rna_by_id.items():
    ambiguous_rna_by_id[key] = Translator(value)

Generated by  Doxygen 1.6.0   Back to index