I have the following code to compare the sequence in multiple large files. The below code works fine with some files but I want it to execute for any number of files however large it may be. I tried executing it with more than 10GB data but the program gets killed. Example of a file is shown below. The count is summed only if the second line of each set matches in both files. I want to give the sum of those set whose second line matches in all the files. 


data1.txt
@NS500278
AGATCNGAA
+
=CCGGGCGG   1

@NS500278
TACAGNGAG
+
CCCGGGGGG   2

@NS500278
CATTGNACC
+
CCCGGGGGG   3

data2.txt

@NS500278
AGATCNGAA
+
=CCGGGCGG   1

@NS500278
CATTGNACC
+
CCCG#GGG#   2

@NS500278
TACAGNGAG
+
CC=GGG#GG   2


output:

@NS500278
AGATCNGAA
+
=GGGGGCCG     1:data1.txt.out    1:data2.txt.out    count:2

@NS500278
CATTGNACC
+
CCCGGGGGG 3:data1.txt.out     2:data2.txt.out    count:5

@NS500278
TACAGNGAG
+
CCCGGGGGG 2:data1.txt.out     2:data2.txt.out    count:4

[download]
My code is: 
#!/usr/bin/env perl
use strict;
use warnings;

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 Re^2: storing hash in temporary files to save memory usage by Anonymous Monk
in thread storing hash in temporary files to save memory usage by Anonymous Monk

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