Thank you bichonfrise74. Your suggestion works very well. It is much simpiler and quite a bit faster than what I was using:

#!/usr/bin/perl
use warnings;
use strict;

my $idfile = 'C:...';
open(ID, $idfile) or die "Cannot open file '$idfile' \n\n";

 #Create and open output file
my $out = 'C:\Users\Clayton\Documents\Research\GO\Data\chr_8\chr_8_pos
+gen';
open (OUT, ">$out");

# Create Variables
my $line;
my $line2;
my %hash = ();

# Read in file line by line
while ( $line = <ID> ) {
    chomp $line;
    # Split the tab delimited file into an array
    my @arr = split /\t/, $line;
    #if(defined($arr[2])){
    # Put the columns of the array into variables
    my $id = $arr[0];
    my $catg_id = $arr[1];
    my $pos = $arr[2];
    
    $hash{$id} = "$catg_id\t$pos";
    
}
close ID;

my @k = keys %hash;
my $k;

my $namefile = 'C:...';
open(NAMEFILE, $namefile) or die "Cannot open file '$namefile' \n\n";

while ( $line2 = <NAMEFILE> ) {
    chomp $line2;
    
    my @loc = split /\t/, $line2;
    
    foreach $k (@k) {
        my @arr2 = split /\t/, $hash{$k};
        if($loc[0] == $arr2[0]){
            if(($arr2[1] >= $loc[1]) and ($arr2[1] <= $loc[2])){
                print OUT "$arr2[0]\t$k\t$arr2[1]\t$loc[1]\t$loc[2]\t$
+loc[3]\n"
            
}}}}

[download]

I'm still new to perl so I guess a lot of my methods are not the most efficient.

One more question though... Whenever I use your code or mine I get an error "Use of uninitialized value in numeric gt (>)at C:\...line 32, <NAMEFILE> line 1. This error repeats many times for each line in the file. The output is what I expect it to be though and the program runs without any problems (other than generating a bunch of warnings).

In reply to Re^2: Comparing multiple entries from two files by hanger4
in thread Comparing multiple entries from two files by hanger4

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