add_mate_reads.py

Say you have a foward read and you want to fetch its corresponding paired-end read. This script does just that, in batch. You provide a FASTQ file containing a subset of forward and reverse reads (or either thereof), and this script extracts the corresponding mates from the parent FASTQ files. A new pair of FASTQ files will be written (forwards reads and reverse reads files), sorted by query-name. This only works for Illumina formatted reads (with regard to the header lines).

usage: add_mate_reads.py [-h] -q QUERY_READS -f FORWARD_READS -r REVERSE_READS
                         --outfile-f OUTFILE_F --outfile-r OUTFILE_R

Named Arguments

-q, --query-reads
	The FASTQ file containing forward, reverse, or a mix of forward and reverse reads whose mates need to be also fetched.
-f, --forward-reads
	The parent foward reads FASTQ file
-r, --reverse-reads
	The parent reverse reads FASTQ file
--outfile-f	Name of the output file for the foward extracted READS (includes any forward reads present in the query set).
--outfile-r	Name of the output file for the reverse extracted READS (includes any reverse reads present in the query set).