merge multiple files based on first column and save memory issues

Question

I have multiple tab delimited fastq files. I want to match the second line of each read and add up the values next to it if it matches. for example:


file1.fq
>1
ATGCCGTT      file1:1
+
HHHHKKKK

file2.fq
>2
ATGCCGTT       file2:3
+
JJKHHTTT

>3
ATTCCAAC        file2:1
+
=#GJLMNB

The output I want is like:


output.txt

ATGCCGTT      file1:1    file2:3     count:4
ATTCCAAC      file2:1          count:1

The code I have written is:



#!/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";
    }
}

This code works well for small files but when I want to compare large files it occupies the whole memory resulting into the script running without results. I want to modify the script so that it does not occupy memory. I don't want to use any modules. I think if I load only one file in memory at a time, it will save memory but unable to do it. Please help modifying my script.

Valentin B. · Accepted Answer · 2016-10-27 09:18:34Z

Have you tried awk ? Not sure it will handle large files better than perl but it might be worth a try:

Inside your awk script:

BEGIN {
    RS=">[0-9]+"
}

FNR==1{next}

NR==FNR {
    a[$1]++
    next
}


$1 in a {
    b[$1]++
    next
}

{
    c[$1]++
}

END {
    for (key in a) {
        if (b[key] == "") {
            printf key"\tfile1:"a[key]"\t\tcount:"a[key]"\n"
        } else {
            printf key"\tfile1:"a[key]"\tfile2:"b[key]"\tcount:"a[key]+b[key]"\n"
        }
    }
    for (key in c) {
        printf key"\t\tfile2:"c[key]"\tcount:"c[key]"\n"
    }
}

To run it:

$ awk -f myscript.awk file1 file2 > output.txt

Tested it with:

file1

>1
ATGCCGTT      file1:1
+
HHHHKKKK

>2
ATTCCAACg        file2:1
+
=#GJLMNB

file2

>2
ATGCCGTT       file2:3
+
JJKHHTTT

>3
ATTCCAAC        file2:1
+
=#GJLMNB

Output in terminal:

ATTCCAACg   file1:1         count:1
ATGCCGTT    file1:1 file2:1 count:2
ATTCCAAC            file2:1 count:1

Nadreck · Accepted Answer · 2017-05-19 08:04:48Z

Add these mystic incantations to your program

use DB_File;
my %seen; 
unlink '/tmp/translation.db';
sleep 2; 
tie ( %seen, 'DB_File', '/tmp/translation.db' )
    or die "Can't open /tmp/translation.db\n";

and your hash will no longer be resident in memory but in a database on disk. You can leave the rest of your code exactly as is. True, I used the DB_File module but there's really no reason not to. It comes with every perl installation out of the box so you don't have to install it or anything.

I use this approach all the time if my hashes are getting really huge and I find that, after passing some hazily defined point of hughness, things speed up quite a bit.

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