I have some realy simple code that just doesn't seem to work when I try using a variable regex. Literal regex works fine.

Here's my code: 


#!/usr/bin/perl -w                 

my $seq;

open (SEQ, "<$ARGV[0]");
open (REP, "<$ARGV[1]");
open (OUT, ">$ARGV[2]");

while (<SEQ>){
    $seq = $_;
    while (<REP>){
        print OUT if /$seq/;
    }

}

close (SEQ);
close (REP);
close (OUT);

[download]
Right now I am just getting an empty file for an output. If I replace /$seq/ with /AAA/ or any other literal, it works just fine.

I'm sure its something easy, but I've been googling all afternoon to no avail.

Here are examples of the contents of the SEQ and REP files: 


SEQ:
AELIVQPELK

REP:
1    116.68    116.68    48.2199996709824    26.8999993801117    21.17
+99994111061    ENST00000379802_141    [201 - 8954] cdna:known chromos
+ome:GRCh37:6:7541808:7586950:1 gene:ENSG00000096696 gene_biotype:prot
+ein_coding transcript_biotype:protein_coding            2    99.00000
+09536743    AELIVQPELK            -5.64623987884261E-05    1138.65991
+210938    570.3372    1138.65979003906    570.337158203125    2    14
+    2.1.1.3480.1    1    0.7224    -1    -1

[download]
Thanks for your help!

Update: Got what I wanted with the following code. Thanks for the input everyone, it was helpful. I was unaware of the mechanics of a while loop using an open file as a condition. I'm sure its still a little messy but I'm a biologist not a programmer, so what can you expect? 

#!/usr/bin/perl -w                 
use strict;
my (@seq, @rep, $i, $n, $l, $t);

open (SEQ, "<$ARGV[0]");
open (REP, "<$ARGV[1]");
open (OUT, ">$ARGV[2]");


$i=0;
$n=0;
$l=0;




while (<SEQ>){
    chomp();
    $seq[$i] = $_;
    $i++;
}
while (<REP>){
    $rep[$n] = $_;
    $n++;

}
while ($l < $i){
    $t=0;
    while ($t < $n){
        print OUT $rep[$t] if $rep[$t] =~ /$seq[$l]/;
        $t++;
    }
    $l++;
}




close (SEQ);
close (REP);
close (OUT);

[download]

In reply to Simple filter from rows of input file by ablakely

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