Off topic:Find The Match Entries In The Columns And Print Them Out By Perl

Question

[Ar Es]

Hi, I have asked this question before , but as Admin said If i want to change my question , I have to ask new question instead of asking by answering the previous one, Anyhow, my question is :

I want to read through 2 different tab-delimited files of sequence coordinates and find the same columns entries in both files and print it out , one file is ref and the other one contains the the columns that I want to find in the ref file : I want to keep col1 - col2 and col3 of file one (ref file) and col1 - col2 - col 3 of file2

file one (ref file) :

Col1      Col2       Col3     Col4  Col5 ColX
chr        start       end    (rest columns)


file2 :

Col1      Col2       Col3     Col4  Col5 ColX
chr        start       end    (rest columns)

I have written script but I got error when i print it out :

Use of uninitialized value $line2 in split at ./match3.pl line 19, <$fh2> line 2458. Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value in string eq at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value $values2[0] in concatenation (.) or string at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value in concatenation (.) or string at ./match3.pl line 22, <$fh2> line 2458. Use of uninitialized value in concatenation (.) or string at ./match3.pl line 22, <$fh2> line 2458.

my script is :

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

open my $fh1, '<', 'file1';
open my $fh2, '<', 'file2';

my$line1 ;
my$line2 ;

while (<$fh1>) {
  chomp;
  my @values1 = split( "\t", $line1 );
  close $fh1;
  while (<$fh2>) {
  chomp;
    my @values2 = split( "\t", $line2 );
close $fh2; 

if ( $values1[0] eq $values2[0] and $values1[1] eq $values2[1] and $values1[2] eq $values2[2])

{
  print "$values2[0] \t $values2[1] \t $values2[2] \t \n" ;}}}

Thanks In Advance,