Re: compare two files by column and return second (matching) column

[aitap]

Firstly, a couple of advices:

my $in1 = $ARGV[0];
my $in2 = $ARGV[1];
my $fout = $ARGV[2];

It can be simplified into: my ($in1, $in2, $fout) = @ARGV;

open ONE, $in1;
open TWO, $in2;
open foutname, ">$fout";

You need to check for errors; it's also safer to use three-argument form of open() (imagine someone specifying '/bin/rm -rf / |' as file name). Thus,

open my $one, '<', $in1 || die "$in1: $!\n";
open my $two, '<', $in2 || die "$in2: $!\n";
open my $foutname, ">", $fout || die "$fout: $!\n";

Secondly, when you need to match something to something, think of a hash. Thus,

my %first;
while (<$one>) {
 chomp;
 my @data = split /\t/;
 $first{$data[0]}=$data[1]; # fill the hash with the values from the f
+irst file
}
close $one;

while (<$two>) {
 chomp; # just search the hash for these strings
 exists $first{$_} && print $foutname $first{$_},'\n';
}
close $two;
close $foutname || warn "$fout: $!\n';

(the code is untested, feel free to ask about errors it gives)