Hi all,

I am having two input files where I have to match columns 1,2,3 of one infile with columns 2,3,4 of second and i have to print for the matched lines the values in column 4 of second infile. I have made two separate arrays for each infile . Here is the script below : 

use strict;
use warnings;

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

unless (open( INFILE1, $infile1)) {
             die "Cannot open $infile1\n";
            }
my @array;
my @slice;
my @array1;
my @slice1;
my $element;

while(<INFILE1>) {
     chomp;
     my @array = split ('\t', $_);
     my @slice = @array[0,1,2];
}
open (INFILE2, "<", $infile2) || die "cannot open $infile2";
open (OFILE, ">", $outfile) || die "cannot open $outfile";

my $i = 0;
while (<INFILE2>) {
        chomp;
        my @array1 = split ('\t', $_);
        my @slice1 = @array1[1,2,3,4];
        $slice1[0] = s/chr//g;
        for ($i=0; $i < $#slice1; $i++) {
        foreach my $element (@slice) {
        print OFILE $slice1[3] ."\n";
        }
        else {
        print OFILE "NA\n";
        }
       }
      }
}

[download]

Any help would be appreciated. Thanks

In reply to Matching columns between files by gggg

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