fastq_clean_pairs.pl

#!/usr/bin/perl
# ejr - 20120216
# open two fastq files, write matching pairs to right and lefts files and then
# unpaired to a third file
# inefficient IO, but has a lower memory footprint for big files
# I should find a better way to do this. BerkeleyDb and SQlite are slower
use strict;
use warnings;
use File::Spec;
use Getopt::Long;

##$file_1 and _2 should be mate fq files
my $file_1;
my $file_2;

GetOptions(
  '1|file_1:s' => \$file_1,
  '2|file_2:s' => \$file_2,
  'h|help'     => \&getHelp,
);

sub getHelp {
  print "
This script takes 2 paired fastq files and matches mates and prints unPaired reads to STDOUT. 
Please name the fastq files with .fq extention.
usage:
./clean_pairs.pl [-1 fastq file 1] [-2 fastq file 2][-h] 

options:
-1 STR          fq file 1 [required, no default]
-2 STR          fq file 2 [required, no default]
-h              this message
";
  exit 1;
}


if ( !defined $file_1 and !defined $file_2 ) {
  print "\n\nMust provide a two files containing paired reads\n\n";
  &getHelp;
  exit 1;
}

my $file_1_path = File::Spec->rel2abs($file_1);
my $file_2_path = File::Spec->rel2abs($file_2);

my $sample;
##sample_1.fq
##sampe_pair1.fq
if ( $file_1 =~ /(\S+?)_?(\S+)\.(fq|fastq)/ ) {
  $sample = $1;
}


my $fq_1 = $file_1;
my $fq_2 = $file_2;
$fq_1 =~ s/(\.fq|\.fastq)$//;
$fq_2 =~ s/(\.fq|\.fastq)$//;


my %lefts;
my %rights;

open (LEFT, $file_1) or die "cannot open $file_1:$!\n";
open (RIGHT, $file_2) or die "cannot open $file_2:$!\n";
open (LEFTOUT, ">$fq_1.matched.fq") or die "cannot open file:$!\n";
open (RIGHTOUT, ">$fq_2.matched.fq") or die "cannot open file:$!\n";

while (my $left_header = <LEFT>) {
       $lefts{$left_header} = 1;
       <LEFT>;
       <LEFT>;
       <LEFT>;
}

close LEFT;

while (my $right_header = <RIGHT>) {
       my $right_seq = <RIGHT>;
       my $right_qual_header = <RIGHT>;
       my $right_qual = <RIGHT>;
       my $right_full = $right_header.$right_seq.$right_qual_header.$right_qual;
           if (exists($lefts{$right_header})){
               print RIGHTOUT $right_full;
               $rights{$right_header} = 1;
           } else {
               print $right_full;
           }
}
close RIGHT;

open (LEFT, $file_1) or die "cannot open $file_1:$!\n";
#open (LEFT, $ARGV[0]) or die "cannot open file:$!\n";



while (my $left_header = <LEFT>) {
       my $left_seq = <LEFT>;
       my $left_qual_header = <LEFT>;
       my $left_qual = <LEFT>;
       my $left_full =$left_header.$left_seq.$left_qual_header.$left_qual;
       if ($rights{$left_header}) {
           print LEFTOUT $left_full;
       } else {
           print $left_full;
       }
}