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#!/usr/bin/env python | |
# -*- coding: utf-8 -*- | |
# Copyright (C) 2010 - 2012, A. Murat Eren | |
# | |
# This program is free software; you can redistribute it and/or modify it under | |
# the terms of the GNU General Public License as published by the Free | |
# Software Foundation; either version 2 of the License, or (at your option) | |
# any later version. | |
# | |
# Please read the COPYING file. | |
import sys | |
import Oligotyping.lib.fastalib as u | |
import Oligotyping.utils.utils as utils | |
progress = utils.Progress() | |
run = utils.Run() | |
# get read length | |
fasta = u.SequenceSource(sys.argv[1], lazy_init = False) | |
fasta.next() | |
len_fasta_entry = len(fasta.seq) | |
# reset fasta. | |
fasta.reset() | |
# make sure all reads have equal length | |
while fasta.next(): | |
if len(fasta.seq) != len_fasta_entry: | |
sys.stderr.write('All reads must have equal number of characters, but it is not the case. Sorry and bye.\n') | |
sys.exit() | |
fasta.reset() | |
# -*- | |
nucleotide_positions = set(range(0, len_fasta_entry)) | |
invalid_columns = set(range(0, len_fasta_entry)) | |
progress.new('Step 1') | |
while fasta.next(): | |
if fasta.pos % 100 == 1: | |
progress.update('%.2d%% -- pos: %d' % (fasta.pos * 100 / fasta.total_seq, fasta.pos)) | |
for i in nucleotide_positions: | |
if fasta.seq[i] != '-' and i in invalid_columns: | |
invalid_columns.remove(i) | |
progress.end() | |
fasta.reset() | |
# -*- | |
columns_to_keep = [x for x in range(0, len_fasta_entry) if x not in invalid_columns] | |
f = open(sys.argv[1] + '-TRIMMED', 'w') | |
progress.new('Step 2') | |
while fasta.next(): | |
if fasta.pos % 100 == 1: | |
progress.update('%.2d%% -- pos: %d' % (fasta.pos * 100 / fasta.total_seq, fasta.pos)) | |
new_seq = ''.join(fasta.seq[i] for i in columns_to_keep) | |
f.write('>' + fasta.id + '\n') | |
f.write(new_seq + '\n') | |
f.close() |
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