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| import data |
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| __all__ = ["revcomp", "translate"] |
|
|
| def revcomp(seq): |
| return seq.translate(data.TRANSTABLE)[::-1] |
|
|
| CODON_TABLES = {} |
| def translate(seq, table=1, start=0, modifications=None, partial=False): |
| if start > 0: |
| seq = seq[start:] |
| if modifications is None: |
| modifications = [] |
| if isinstance(partial, bool): |
| partial = (partial, partial) |
| if table not in CODON_TABLES: |
| raise ValueError("Unknown translation table: %s" % table) |
| if len(seq) < 3: |
| raise ValueError("Sequnce length is too short.") |
| t = CODON_TABLES[table] |
| (acid, is_start) = t.translate(seq[:3], len(seq) == 3) |
| if not partial[0] and is_start: |
| ret = ["M"] |
| elif not partial[0] and start < 1: |
| ret = ["X"] |
| else: |
| ret = [acid] |
| seqlen = len(seq) |
| for i in xrange(3, seqlen-(seqlen%3), 3): |
| ret.append(t.translate(seq[i:i+3], i == len(seq) - 3)[0]) |
| ret = ''.join(ret) |
| for m in modifications: |
| if m[0] % 3 != 0: |
| raise ValueError("Invalid modification coordinate: %s" % m[0]) |
| idx = m[0]/3 |
| ret = "%s%s%s" % (ret[:idx], m[1], ret[idx+1:]) |
| if not partial[1] and ret[-1:] == "*": |
| ret = ret[:-1] |
| return ret |
|
|
| class TranslationTable(object): |
| def __init__(self, codons, starts): |
| self.codons = codons |
| self.starts = starts |
| def translate(self, codon, is_stop): |
| assert len(codon) == 3, "Invalid codon: %s" % codon |
| degen = map(lambda b: data.DEGENERATES.get(b, b), codon) |
| degencodons = [ |
| "%s%s%s" % (b1, b2, b3) |
| for b1 in degen[0] |
| for b2 in degen[1] |
| for b3 in degen[2] |
| ] |
| acids = set(map(lambda x: self.codons.get(x, 'X'), degencodons)) |
| starts = set(map(lambda x: self.starts.get(x, False), degencodons)) |
| if len(acids) == 1 and acids == set("*") and not is_stop: |
| acid = "X" |
| elif len(acids) == 1: |
| acid = acids.pop() |
| elif acids == set("DN"): |
| acid = "B" |
| elif acids == set("EQ"): |
| acid = "Z" |
| elif acids == set("IL"): |
| acid = "J" |
| else: |
| acid = "X" |
| if len(starts) > 1: |
| start = False |
| else: |
| start = starts.pop() |
| return (acid, start) |
| |
| for tbl in [t.split() for t in data.CODON_TABLE_DATA]: |
| tid = int(tbl[0]) |
| trans = dict(zip(data.CODONS, tbl[1])) |
| starts = dict(zip(data.CODONS, map(lambda x: x == "M", tbl[2]))) |
| CODON_TABLES[tid] = TranslationTable(trans, starts) |
|
|
