I have two files and I want to merge the common lines as well as print the uncommon ones. I have written a code which is working but I would like to have some better way to do it. The code I have written is : 
@files = @ARGV;
$size = @files;


open (FA, ">>comp.txt");

open (FH, @ARGV[0]);
while ($seq = <FH>)
{ chomp $seq;
@seq = split ("\t", $seq);

$seqm = @seq[0];
chomp $seqm;
open (FH1, @ARGV[1]);

while ($seq2 = <FH1>)
{ chomp $seq2;
@seq2 = split ("\t", $seq2);

$seqm1 = @seq2[0];
chomp $seqm1;
if ($seqm1 =~m/$seqm/)
{$names=$names."\n".$seq."\t".@seq2[1]."\n";
$c=1;
last;}
else {$c=0;}

}
if ($c=="0")
{$names=$names."\n".$seq."\n";}
}

open (FH, @ARGV[1]);
while ($seq = <FH>)
{ chomp $seq;
@seq = split ("\t", $seq);

$seqm = @seq[0];
chomp $seqm;
open (FH1, @ARGV[2]);

while ($seq2 = <FH1>)
{ chomp $seq2;
@seq2 = split ("\t", $seq2);

$seqm1 = @seq2[0];
chomp $seqm1;
if ($seqm1 =~m/$seqm/)
{
$c=1;
last;}
else {$c=0;}

}
if ($c=="0")
{$names1=$names1."\n".$seq."\n";}
}
print FA $names."\n".$names1;

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In reply to find unique lines in two files by Anonymous Monk

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