Hi, I am trying to match the three columns (first three) of one file with the columns 0,3,4 of the second file using perl.My code so far is 

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

my $infile1 = $ARGV[0];
my $infile2 = $ARGV[1];
my $outfile = $ARGV[2];

open (INFILE1,"<", $infile1) || die "Cannot open $infile1:$!\n";
open (INFILE2, "<", $infile2) || die "Cannot open $infile2:$!\n";
open (OUTFILE, ">", $outfile) || die "Cannot open $outfile:$!\n";

my @array1;
my @array2;
my @array3;
my @array4;
my $_;
while (<INFILE1>) {
        chomp;
        @array1 = split (' ', $_);
        push (@array2, "@array1\n");
        #print "@array2\n";
}
while (<INFILE2>) {
        chomp;
        @array3 = split (' ', $_);
        push (@array4, "@array3\n");
        #print "@array4\n";
}
#print "@array2\n";
#print "@array4\n";
foreach my $array2(@array2) {
   my @line = split(/\s+/,$array2);
   my $chr1 = $line[0];
   my $start1 = $line[1];
   my $end1 = $line[2];
   #print "$line[0]\n";
 foreach my $array4(@array4) {
  my @values = split(/\s+/, $array4);
   my $chr2 = $values[0];
   my $start2 = $values[3];
   my $end2 = $values[4];
   if (($chr1 eq $chr2 ) && ($start1 eq  $start2) && ($end1 eq $end2))
+ {
       #print  "$start2\n";
        print  "$chr2\t$start2\t$end2\n";
   }

}
}

[download]

please help me with this code.Thanks.

In reply to Compare three columns of one file with three columns of another file in perl by anonym

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