Hi monks, I wondered if I could have some help using flags.

I am simply checking through a file of records, looking for any that match and then extracting that particular record.

My problem is that if I find one that matches, my code takes all the records from then onwards, regardless of whether they pass the criteria.

The file of records looks something like this:

>RC|ae000001||99-143
ACGFEHIGJUHIDFHDIHGFHHIIFHIHHFBIHB
DHFIJHGIJFIGKFKPDOKFKFKFFFFF
>RC|ae000002|150-179
THDFHOIHDIOVIJJOFPJGFJVOKVKFFKBDJK
HHTHTHTHAAAAA
>RC|ae000003|185-207
KLJDJFGJFJDJFKJKJFSJFKDHSHKFJKDJDK
SAJSAJJSDSPIDOSDKSKFKF
[download]

I am simply trying to check the numbers (e.g 99-143) against an array of numbers and pull out that particular record if it matches. Please have a look at my code to see where i'm going wrong: Many thanks

foreach my $l (@file)  {

    if (($l =~ /^>(\w{2})(.{1})(\w{2}\d{6}.{2})(\D?)(\d+)(\W{1})(\d+)/
+))   {

        $current =  undef;

        if ($4)   {
            $hit = "$7-$5";
        }

        else {
             $hit = "$5-$7";
        }
}

    foreach my $k (@positions)   {
        if ($k == $hit)  {
            $in_gene = 1;
        }
    }

     if ($in_gene)   {
          $gene .= $l;
     }

     unless ($l =~ /^>/)  {
         next;
     }

}
print $gene;
[download]