Here is some code to show you perl idioms on how to approach this problem. 
#!usr/bin/perl
use strict;
use warnings;

my ($infile1 ,$infile2) = @ARGV;

open (my $in1 ,"<", $infile1) or die "Cannot open '$infile1':$!\n";
open (my $in2, "<", $infile2) or die "Cannot open '$infile2':$!\n";
my @values;
while ( <$in1> ){
  chomp;
  my @one = split;
  next unless scalar(@one) >= 3; # Must have at least 3 
  push @values, [@one[0..2]];
}
close $in1;

while (<$in2>){
    chomp;
    my @two = split;
    next unless scalar(@two) >= 5; # Must have at least 5
    next unless grep { 
               $_->[0] eq $two[0]  
           and $_->[1] eq $two[3]
           and $_->[3] eq $two[4]
      } @values;
    print join("\t",@two[0,3,4]) , "\n"
}
close $in2;

[download]
You will need to understand "array slices", and references.

        "You're only given one little spark of madness. You mustn't lose it."         - Robin Williams

In reply to Re: Compare three columns of one file with three columns of another file in perl by NetWallah
in thread Compare three columns of one file with three columns of another file in perl by anonym

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