open my $fhConditions, "<", "1.txt" or die "Epic Fail: $!";
use strict;
use warnings;
open my $fhCharacters, "<", "2.txt" or die "OMG Fail: $!";
my $length = 250;
while (my $line = <$fhConditions>) {
    chomp $line;
my ($strand, $chr, $position) = split(' ', $line);     
    $position += $length    if $strand == 0;
    $position -= $length    if $strand == 1;
    seek $fhCharacters, $position, 0;
    my $data;
    read $fhCharacters, $data, $length;
    if ($data =~ m/$AAGCTT/) {
        print "Y" "\n";
        else 
        print "N" "\n";
    }
}

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this is the code i derived from urs.

wen i am running it gives error like : Missing $ on loop variable at restriction.pl line 8.

In reply to Re^2: matchin a pattern 250 characters up and down stream by Anonymous Monk
in thread matchin a pattern 250 characters up and down stream by Anonymous Monk

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