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#!/usr/bin/env python
# Copyright 2000 by Thomas Sicheritz-Ponten.
# Copyright 2016 by Markus Piotrowski.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# Created: Wed Jun 21 15:53:22 2000
# thomas@cbs.dtu.dk, http://www.cbs.dtu.dk/thomas
# File: xbb_translations.py
from __future__ import print_function
import time
from Bio.Seq import Seq, reverse_complement, translate
from Bio.SeqUtils import GC
class xbb_translations(object):
def __init__(self):
pass
def frame1(self, seq, translation_table=1):
return translate(seq, table=translation_table)
def complement(self, seq):
return Seq.complement(Seq(seq))
def reverse(self, seq):
return seq[::-1]
def antiparallel(self, seq):
return reverse_complement(seq)
def frame(self, seq, frame, translation_table=1):
if frame < 0:
seq = reverse_complement(seq)
seq = seq[(abs(frame) - 1):]
return translate(seq, table=translation_table)
def header_nice(self, txt, seq):
length = len(seq)
if length > 20:
short = '%s ... %s' % (seq[:10], seq[-10:])
else:
short = seq
date = time.strftime('%y %b %d, %X', time.localtime(time.time()))
res = '%s: %s, ' % (txt, date)
for nt in ['a', 't', 'g', 'c']:
res += '%s:%d ' % (nt, seq.count(nt.upper()))
res += '\nSequence: %s, %d nt, %0.2f %%GC\n' % (short.lower(),
length, self.gc(seq))
res += '\n\n'
return res
def frame_nice(self, seq, frame, translation_table=1):
length = len(seq)
protein = self.frame(seq, frame, translation_table)
protein_length = len(protein)
protein = ' '.join([aa for aa in protein])
protein += (((length - (abs(frame) - 1)) % 3) + 2) * ' '
if frame < 0:
protein = protein[::-1]
res = self.header_nice('Frame {} translation'.format(frame), seq)
for i in range(0, length, 60):
subseq = seq[i:i + 60]
p = i // 3
if frame > 0:
res += '%d/%d\n' % (i + 1, p + 1)
res += ' ' * (frame - 1) + protein[i:i + 60] + '\n'
# seq
res += (subseq.lower() + '%5d %%\n' % int(self.gc(subseq)) +
'\n')
else:
res += '%d/%d\n' % (i + 1, protein_length -
len(protein[:i].split()))
# seq
res += subseq.lower() + '%5d %%\n' % int(self.gc(subseq))
res += protein[i:i + 60] + '\n\n'
return res
def gc(self, seq):
"""Returns a float between 0 and 100."""
return GC(seq)
def gcframe(self, seq, translation_table=1, direction='both'):
# always use uppercase nt-sequence !!
comp = self.complement(seq)
anti = self.reverse(comp)
length = len(seq)
frames = {}
for i in range(0, 3):
frames[i + 1] = self.frame1(seq[i:], translation_table)
frames[-(i + 1)] = self.reverse(self.frame1(anti[i:],
translation_table))
res = self.header_nice('GCFrame', seq)
for i in range(0, length, 60):
subseq = seq[i:i + 60]
csubseq = comp[i:i + 60]
p = i // 3
if direction in ('plus', 'both'):
# + frames
res += '%d/%d\n' % (i + 1, i // 3 + 1)
res += ' ' + ' '.join(frames[3][p:p + 20]) + '\n'
res += ' ' + ' '.join(frames[2][p:p + 20]) + '\n'
res += ' '.join(frames[1][p:p + 20]) + '\n'
# seq
res += subseq.lower() + '%5d %%\n' % int(self.gc(subseq))
res += csubseq.lower() + '\n'
if direction == 'plus':
res += '\n'
if direction in ('minus', 'both'):
# - frames
res += ' '.join(frames[-2][p:p + 20]) + ' \n'
res += ' ' + ' '.join(frames[-1][p:p + 20]) + '\n'
res += ' ' + ' '.join(frames[-3][p:p + 20]) + '\n\n'
return res
if __name__ == '__main__':
s = 'ATTCCGGTTGATCCTGCCGGACCCGACCGCTATCGGGGTAGGGATAAGCCATGGGAGTCT' \
'TACACTCCCGGGTAAGGGAGTGTGGCGGACGGCTGAGTAACACGTGGCTAACCTACCCTC' \
'GGGACGGGGATAACCCCGGGAAACTGGGGATAATCCCCGATAGGGAAGGAGTCCTGGAAT' \
'GGTTCCTTCCCTAAAGGGCTATAGGCTATTTCCCGTTTGTAGCCGCCCGAGGATGGGGCT' \
'ACGGCCCATCAGGCTGTCGGTGGGGTAAAGGCCCACCGAACCTATAACGGGTAGGGGCCG' \
'TGGAAGCGGGAGCCTCCAGTTGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCACC' \
'AGGCGCGAAACGTCCCCAATGCGCGAAAGCGTGAGGGCGCTACCCCGAGTGCCTCCGCAA' \
'GGAGGCTTTTCCCCGCTCTAAAAAGGCGGGGGAATAAGCGGGGGGCAAGTCTGGTGTCAG' \
'CCGCCGCGGTAATACCAGCTCCGCGAGTGGTCGGGGTGATTACTGGGCCTAAAGCGCCTG' \
'TAGCCGGCCCACCAAGTCGCCCCTTAAAGTCCCCGGCTCAACCGGGGAACTGGGGGCGAT' \
'ACTGGTGGGCTAGGGGGCGGGAGAGGCGGGGGGTACTCCCGGAGTAGGGGCGAAATCCTT' \
'AGATACCGGGAGGACCACCAGTGGCGGAAGCGCCCCGCTA'
test = xbb_translations()
print('============================================================')
print(test.gcframe(s))
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