File size: 2,709 Bytes
b2e2343 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | # Copyright 2009 New England Biolabs <davisp@neb.com>
#
# This file is part of the BioNEB package released
# under the MIT license.
#
import data
__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)
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