Firstly, a couple of advices: 
my $in1 = $ARGV[0];
my $in2 = $ARGV[1];
my $fout = $ARGV[2];

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It can be simplified into: my ($in1, $in2, $fout) = @ARGV; 
open ONE, $in1;
open TWO, $in2;
open foutname, ">$fout";

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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";

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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';

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(the code is untested, feel free to ask about errors it gives)
Sorry if my advice was wrong.

In reply to Re: compare two files by column and return second (matching) column by aitap
in thread compare two files by column and return second (matching) column by ejbiers

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