annotate FilterUncorrectabledPEfastq.py @ 1:6703b98884a2 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit 65ada0f9589f3ffebad1db6636ccb50d58082606"

"""
author: adam h freedman
afreedman405 at gmail.com
data: Fri Aug 26 10:55:18 EDT 2016
This script takes as an input Rcorrector error corrected Illumina paired-reads
in fastq format and:
1. Removes any reads that Rcorrector indentifes as containing an error,
but can't be corrected, typically low complexity sequences. For these,
the header contains 'unfixable'.
2. Strips the ' cor' from headers of reads that Rcorrector fixed, to avoid
issues created by certain header formats for downstream tools.
3. Write a log with counts of (a) read pairs that were removed because one end
was unfixable, (b) corrected left and right reads, (c) total number of
read pairs containing at least one corrected read.
Currently, this script only handles paired-end data, and handle either unzipped
or gzipped files on the fly, so long as the gzipped files end with 'gz'.
"""

import argparse
import gzip
from itertools import zip_longest
from os.path import basename


def get_input_streams(r1file, r2file):
    if r1file[-2:] == 'gz':
        r1handle = gzip.open(r1file, 'rb')
        r2handle = gzip.open(r2file, 'rb')
    else:
        r1handle = open(r1file, 'r')
        r2handle = open(r2file, 'r')
    return r1handle, r2handle


def grouper(iterable, n, fillvalue=None):
    "Collect data into fixed-length chunks or blocks"
    # grouper('ABCDEFG', 3, 'x') --> ABC DEF Gxx
    args = [iter(iterable)] * n
    return zip_longest(fillvalue=fillvalue, * args)


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="options for filtering and logging rCorrector fastq outputs")
    parser.add_argument('-1', '--left_reads', dest='leftreads', type=str, help='R1 fastq file')
    parser.add_argument('-2', '--right_reads', dest='rightreads', type=str, help='R2 fastq file')
    parser.add_argument('-o', '--out_prefix', dest='outprefix', type=str, help="prefix for filtered fastq output")
    opts = parser.parse_args()
    r1out = open(opts.outprefix + '_' + basename(opts.leftreads).replace('.gz', ''), 'w')
    r2out = open(opts.outprefix + '_' + basename(opts.rightreads).replace('.gz', ''), 'w')
    r1_cor_count = 0
    r2_cor_count = 0
    pair_cor_count = 0
    unfix_count = 0
    r1_stream, r2_stream = get_input_streams(opts.leftreads, opts.rightreads)
    with r1_stream as f1, r2_stream as f2:
        R1 = grouper(f1, 4)
        R2 = grouper(f2, 4)
        counter = 0
        for entry in R1:
            counter += 1
            if counter % 100000 == 0:
                print("%s reads processed" % counter)
            head1, seq1, placeholder1, qual1 = [i.strip() for i in entry]
            head2, seq2, placeholder2, qual2 = [j.strip() for j in next(R2)]
            if 'unfixable' in head1 or 'unfixable' in head2:
                unfix_count += 1
            else:
                if 'cor' in head1:
                    r1_cor_count += 1
                if 'cor' in head2:
                    r2_cor_count += 1
                if 'cor' in head1 or 'cor' in head2:
                    pair_cor_count += 1
                head1 = head1.split('l:')[0][:-1]  # keeps all before the low kmer count statistic and removes the trailing whitespace character
                head2 = head2.split('l:')[0][:-1]
                # head1 = head1.replace(' cor', '')
                # head2 = head2.replace(' cor', '')
                r1out.write('%s\n' % '\n'.join([head1, seq1, placeholder1, qual1]))
                r2out.write('%s\n' % '\n'.join([head2, seq2, placeholder2, qual2]))
    unfix_log = open('rmunfixable.log', 'w')
    unfix_log.write('total PE reads:%s\nremoved PE reads:%s\nretained PE reads:%s\nR1 corrected:%s\nR2 corrected:%s\npairs corrected:%s\n' % (counter, unfix_count, counter - unfix_count, r1_cor_count, r2_cor_count, pair_cor_count))
    r1out.close()
r2out.close()