I have multiple files with NGS reads with two columns. The first column contains reads and the second contains the count of that particular read in that file. The files are tab delimited 
eg:
file1
@ns
ATTGCGTTC
+
//#$@TMSQ           2

@ns
GGAGCGTTC
+
//#$@TMSQ           3

[download]
file2
@ns
ATTGCGTTC
+
//#$@#//A           1

[download]

output:

@ns
ATTGCGTTC
+
//#$@TMSQ           2           1      count:3

@ns
GGAGCGTTC
+
//#$@TMSQ           3           count:3

[download]
The program should give the count if second line of each read matches. I have written the following code for this. THe code is working perfectly well but consumes large amount of memory. When I tried the codes for huge files it hangs with no output. Can anyone modify my code so that minimum memory is used. 

#!/usr/bin/env perl
use strict;
use warnings;
no warnings qw( numeric );
my %seen;

$/ = "";
while (<>) {
    chomp;
    my ($key, $value) = split ('\t', $_);

    my @lines = split /\n/, $key;
    my $key1 = $lines[1];

    $seen{$key1} //= [ $key ];
    push (@{$seen{$key1}}, $value);
}

foreach my $key1 ( sort keys %seen ) {
my $tot = 0;
my $file_count = @ARGV;
for my $val ( @{$seen{$key1}} ) {
        $tot += ( split /:/, $val )[0];
    }   
    
if ( @{ $seen{$key1} } >= $file_count) {


        print join( "\t", @{$seen{$key1}});
        print "\tcount:". $tot."\n\n";
    }
}

[download]

In reply to merge multiple files giving out of memory error by Anonymous Monk

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