By using a foreach-loop on the list of file names and using lexical variables, it should be no bigger than this: 
#!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dump qw/dump/;

my %data;

foreach my $filename (qw/one.txt two.txt three.txt/) {
    open( my $file, $filename )
        or die "Unable to open $filename because $!\n";
    while (<$file>) {
        chomp;
        my ( $chrX, $chrpos, $value1, $value2 ) = split(/\s+/);
        $data{$chrX}->{$chrpos}->{'value1'} += $value1;
        $data{$chrX}->{$chrpos}->{'value2'} += $value2;
    } ## end while (<$file>)
} ## end foreach my $filename (qw/one.txt two.txt three.txt/)

print dump( \%data );

[download]
Output:
{
  chromosome1 => { 50000 => { value1 => 64, value2 => 73 } },
  chromosome2 => { 20000 => { value1 => 4,  value2 => 63 } },
  chromosome3 => { 41444 => { value1 => 13, value2 => 28 } },
  chromosome4 => { 21414 => { value1 => 4,  value2 => 1  } },
  chromosome6 => { 12141 => { value1 => 12, value2 => 22 } },
}

[download]

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

In reply to Re: How to add values of hash by reading from different text files by CountZero
in thread How to add values of hash by reading from different text files by faozhi

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