open (my $fhConditions, "<a.txt"); 
my $l=6;
open (my $read, "<b.txt");
my @e = <$read>;
my $d = join('', @e );
$d =~ s/\s+//g;
while (<$fhConditions>) {
    push (my @line, $_);
$count++;
}
for ($i = 0; $i < $count; $i++)
{
my @pos = my $line[$i] =~ /chr*\s+(.+?)\s/g;
if($pos[0] =~/[0-9]/)
{
my $match = substr($d,$pos[0],$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
if($pos[1] =~/[0-9]/)
{
my $a = $pos[0]-$l;
my $match = substr($d,$a,$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
}

[download]
this the code modified after the suggestions. but still i am getting some error 
yntax error at restriction.pl line 13, near "$line["
Execution of restriction.pl aborted due to compilation errors.

[download]

In reply to Re^2: How to get rid of the errors in my perl script by Anonymous Monk
in thread How to get rid of the errors in my perl script by Anonymous Monk

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