#!/usr/bin/perl -w # Copyright 2013 Scott Hunicke-Smith # # #given a fastq file, reverse complement the sequence and reverse the quality (quality in ASCII characters) use strict; my ($rfile, $line, $dna, $revcomp); $rfile=$ARGV[0]; open RFILE, "<$rfile"; while (defined(my $line = <RFILE>)) { chomp($line); my $dna = <RFILE>; #read to be revcomplemented chomp($dna); if ( substr($dna,0,15) eq "CCTATCCCCTGTGTG") { print "$line\n"; #read id print STDERR "$line\n"; #read id my $revcomp = reverse($dna); $revcomp =~ tr/ACGTNacgtn/TGCANtgcan/; print substr($revcomp,42), "\n"; print STDERR substr($revcomp,30,11), "\n"; $line = <RFILE>; #quality id chomp($line); print "$line\n"; print STDERR "$line\n"; my $qual = <RFILE>; chomp ($qual); my $revqual = reverse($qual); print substr($revqual,42),"\n"; print STDERR substr($revqual,30,11), "\n"; } else { if ( substr($dna,0,15) eq "CCATCTCATCCCTGC" ) { print "$line\n"; #read id print STDERR "$line\n"; #read id print substr($dna,42), "\n"; print STDERR substr($dna,30,11), "\n"; $line = <RFILE>; #quality id chomp($line); print "$line\n"; print STDERR "$line\n"; my $qual = <RFILE>; chomp ($qual); print substr($qual,42),"\n"; print STDERR substr($qual,30,11), "\n"; } } }
Manage space
Manage content
Integrations