clean_pairs.pl

#!/usr/bin/perl -w

use strict;
use File::Spec;
use Getopt::Long;

## creates a shell script for converting sam to bam files using samtools

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


##takes a sam file and splits it into separate files based on the
##targets sequences.

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 %pairs;

open INFASTQ_1, "$file_1" or die "problem opening $file_1 $!";
my $fq_1 = $file_1;
my $fq_2 = $file_2;
$fq_1 =~s/\.fq//;
$fq_2=~s/\.fq//;
open OUTFASTQ_1, ">$fq_1.matched.fq";
open OUTFASTQ_2, ">$fq_2.matched.fq";

while ( my $header = <INFASTQ_1> ) {
    chomp $header;
    my $header_to_store;
    if ($header =~ /(\S+)(\.r|\.f)/){
	$header_to_store = $1;
    }elsif($header =~ /(\S+)(\/1|\/2)/){
	$header_to_store = $1;
    }elsif($header =~ /(\S+)/){
       $header_to_store = $1;
    }else{
	$header_to_store = $header;
    }
    my $seq = <INFASTQ_1>;
    warn "$file_1 at record $header has a bad format\n" if !defined $seq;
    chomp $seq;

    my $qual_header = <INFASTQ_1>;
    warn "$file_1 at record $header has a bad format\n" if !defined $qual_header;
    chomp $qual_header;

    my $qual = <INFASTQ_1>;
    warn "$file_1 at record $header has a bad format\n" if !defined $qual;
    chomp $qual;

    $seq = "$header\n$seq\n$qual_header\n$qual" ;
    $pairs{$header_to_store} = $seq;
	
}
if ($file_2 !~ /(fq|fastq)$/){
	die "$file_2 is not a fastq file\n";
} 
open INFASTQ_2, "$file_2"    or die $!;
#open NOMATCH,   ">>$base.noPair.fq" or die $1;
#my $file_1_to_print;
#my $file_2_to_print;
my $no_match_file_to_print;

while ( my $header = <INFASTQ_2> ) {
    chomp $header;
    my $header_to_store;
    if ($header =~ /(\S+)(\.r|\.f)/){
        $header_to_store = $1;
    }elsif($header =~ /(\S+)(\/1|\/2)/){
        $header_to_store = $1;
    }elsif($header =~ /(\S+)/){
       $header_to_store = $1;
    }else {
        $header_to_store = $header;
    }    
    my $seq_2 = <INFASTQ_2>;
    warn "$file_2 at record $header has a bad format\n" if !defined $seq_2;
    chomp $seq_2;
    
    my $qual_header = <INFASTQ_2>;
    warn "$file_2 at record $header has a bad format\n" if !defined $qual_header;
    chomp $qual_header;
    
    my $qual = <INFASTQ_2>;
    warn "$file_2 at record $header has a bad format\n" if !defined $qual;
    chomp $qual;
    $seq_2 = "$header\n$seq_2\n$qual_header\n$qual" ;

    if ( exists $pairs{$header_to_store} ) {
        my $seq_1 = $pairs{$header_to_store};
        print OUTFASTQ_1 "$seq_1\n";
        print OUTFASTQ_2 "$seq_2\n";
        #$file_1_to_print .=  "$seq_1\n";
        #$file_2_to_print .=  "$seq_2\n";

#remove the found keys, so that only the unparied from the first file are in hash at end of loop
        delete $pairs{$header_to_store};
    }
    else {    #print any seq in file2 that was not in file one
        #print  "$seq_2\n";
        $no_match_file_to_print .= "$seq_2\n";
    }
}

#will print any remaing and unpair seqs from the first file into NOMATCH
foreach my $header ( sort keys %pairs ) {
    my $seq = $pairs{$header};
    #print  "$seq\n";
    $no_match_file_to_print .=  "$seq\n";
}

##print matches to files
print $no_match_file_to_print if defined $no_match_file_to_print ;
#print OUTFASTQ_1 $file_1_to_print;
#print OUTFASTQ_2 $file_2_to_print;