#!/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);


##</code><code>##


SEQ:
AELIVQPELK

REP:
1	116.68	116.68	48.2199996709824	26.8999993801117	21.1799994111061	ENST00000379802_141	[201 - 8954] cdna:known chromosome:GRCh37:6:7541808:7586950:1 gene:ENSG00000096696 gene_biotype:protein_coding transcript_biotype:protein_coding			2	99.0000009536743	AELIVQPELK			-5.64623987884261E-05	1138.65991210938	570.3372	1138.65979003906	570.337158203125	2	14	2.1.1.3480.1	1	0.7224	-1	-1


##</code><code>##

#!/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);