You can read the positions into an array by themsevels, and then open the second file and iterate over the array to find lines where the positions are enclosed within the ranges. That way you open each file only once 

use strict;
use warnings;

open(my $fh1, "<","positions.txt") or die("could not open file $!\n");
my @positions;    #hold the positions to be compared
while(my $line=<$fh1>){
    chomp $line;
    push @positions,$line;
    }

open(my $fh2, "<","coords_orientation.txt") or die("could not open fil
+e $!\n");
while(my $line=<$fh2>){
    chomp $line;
    my @record=split(" ",$line); #split the coords_orientation.txt on 
+white space 
    foreach my $pos (@positions){
        if($pos > $record[0] && $pos <$record[1]){
            print "$pos @record\n";        
            }
        }
    }

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A 4 year old monk

In reply to Re: Comparing FILE1 value to FILE2 range and printing matches by biohisham
in thread Comparing FILE1 value to FILE2 range and printing matches by edwardtickle

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