fq.format.pl

#!/usr/bin/perl -w
use Getopt::Long;
my $help;
my $infile="";
my $outfile="";
my $oddlenfile="";

GetOptions(
        "help|h"        => \&USAGE,
        "infile:s"      => \$infile,
        "outfile:s"     => \$outfile,
        "oddlenfile:s"  => \$oddlenfile,
);

open IN,"$infile"||die;
open OUT,">$outfile"||die;
open ODD,">$oddlenfile"||die;

my $i=0;
my $seqID='';
my $sequence='';
my $len_S=0;
my $len_Q=0;
my $mark='';
my $qual='';

while(<IN>){
        chomp;
        if($i%4 == 0){
        $seqID=$_;}
                if($i%4 == 1){
                $sequence=$_;
                $len_S=length($sequence);}
                        if($i%4 == 2){
                        $mark=$_;}
                                if($i%4 == 3){
                                $qual=$_;
                                $len_Q=length($qual);
                                        if($len_S == $len_Q){
                                                print OUT "$seqID\n$sequence\n$mark\n$qual\n";} else {
                                                        print ODD "$seqID\n$sequence\n$mark\n$qual\n";}
                                }
        $i=$i+1
}

sub USAGE{
        my $usage=<<"USAGE";
Program: fa_filter.pl
Date: 2018-07-19
Usage:
                -infile         <fastq format> infile
                -outfile        <fastq format> outfile
                -oddlenfile     <fastq format> oddlenfile
                 -h          help
Example1: perl thir_test.pl -infile data.fastq -outfile out.fastq -oddlenfile odd.fastq
Example2: perl thir_test.pl -h
USAGE
        print $usage;
        exit;
}