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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
"""Translation code for graphical Xbbtools tool."""
import time
from Bio.Seq import reverse_complement
from Bio.Seq import Seq
from Bio.Seq import translate
from Bio.SeqUtils import gc_fraction
class xbb_translations:
"""A class for doing translations."""
def __init__(self):
"""Initialize the class."""
def frame1(self, seq, translation_table=1):
"""Translate first reading frame."""
return translate(seq, table=translation_table)
def complement(self, seq):
"""Return complementary DNA Seq object."""
return Seq.complement(Seq(seq))
def reverse(self, seq):
"""Reverse the sequence."""
return seq[::-1]
def antiparallel(self, seq):
"""Return reverse complementary sequence."""
return reverse_complement(seq)
def frame(self, seq, frame, translation_table=1):
"""Translate DNA sequence in a chosen frame."""
if frame < 0:
seq = reverse_complement(seq)
seq = seq[(abs(frame) - 1) :]
return translate(seq, table=translation_table)
def header_nice(self, txt, seq):
"""Print a short header for the translation window."""
length = len(seq)
if length > 20:
short = f"{seq[:10]} ... {seq[-10:]}"
else:
short = seq
date = time.strftime("%y %b %d, %X", time.localtime(time.time()))
res = f"{txt}: {date}, "
for nt in ["a", "t", "g", "c"]:
res += f"{nt}:{seq.count(nt.upper()):d} "
res += f"\nSequence: {short.lower()}, {length:d} nt, %0.2f %{self.gc(seq):G}C\n"
res += "\n\n"
return res
def frame_nice(self, seq, frame, translation_table=1):
"""Print a pretty print single frame translation."""
length = len(seq)
protein = self.frame(seq, frame, translation_table)
protein_length = len(protein)
protein = " ".join(list(protein))
protein += (((length - (abs(frame) - 1)) % 3) + 2) * " "
if frame < 0:
protein = protein[::-1]
res = self.header_nice(f"Frame {frame} translation", 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):
"""Calculate GC content in percent (0-100)."""
return 100 * gc_fraction(seq)
def gcframe(self, seq, translation_table=1, direction="both"):
"""Print a pretty print translation in several frames."""
# always use uppercase nt-sequence !!
comp = self.complement(seq)
anti = self.reverse(comp)
length = len(seq)
frames = {}
for i in range(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__":
seq = (
"ATTCCGGTTGATCCTGCCGGACCCGACCGCTATCGGGGTAGGGATAAGCCATGGGAGTCT"
"TACACTCCCGGGTAAGGGAGTGTGGCGGACGGCTGAGTAACACGTGGCTAACCTACCCTC"
"GGGACGGGGATAACCCCGGGAAACTGGGGATAATCCCCGATAGGGAAGGAGTCCTGGAAT"
"GGTTCCTTCCCTAAAGGGCTATAGGCTATTTCCCGTTTGTAGCCGCCCGAGGATGGGGCT"
"ACGGCCCATCAGGCTGTCGGTGGGGTAAAGGCCCACCGAACCTATAACGGGTAGGGGCCG"
"TGGAAGCGGGAGCCTCCAGTTGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCACC"
"AGGCGCGAAACGTCCCCAATGCGCGAAAGCGTGAGGGCGCTACCCCGAGTGCCTCCGCAA"
"GGAGGCTTTTCCCCGCTCTAAAAAGGCGGGGGAATAAGCGGGGGGCAAGTCTGGTGTCAG"
"CCGCCGCGGTAATACCAGCTCCGCGAGTGGTCGGGGTGATTACTGGGCCTAAAGCGCCTG"
"TAGCCGGCCCACCAAGTCGCCCCTTAAAGTCCCCGGCTCAACCGGGGAACTGGGGGCGAT"
"ACTGGTGGGCTAGGGGGCGGGAGAGGCGGGGGGTACTCCCGGAGTAGGGGCGAAATCCTT"
"AGATACCGGGAGGACCACCAGTGGCGGAAGCGCCCCGCTA"
)
test = xbb_translations()
print("============================================================")
print(test.gcframe(seq))
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