[Bioperl-l] recursion limit reached for a gbk file

[Dave Messina]

Hi Gopal,

This is not a BioPerl question, so this list is really not the place for it.

However, here's the first Google hit on your error message, which provides a solution:

	http://www.perlmonks.org/?node_id=810857

The short answer is that it's sort of a bug in Perl which is fixed in Perl version 5.12.

Also, this is probably not a good approach for long strings. What is this technique being used for in "Beginning Perl for Bioinformatics"?


Dave



On Jun 10, 2010, at 6:24 PM, Gopal wrote:

> Hi,
> 
> I get a  error message "Complex regular subexpression recursion limit
> (32766) exceeded " when I try to parse CDS from a microbial genbank file.
> Apparently  recursion limit is universal and that means,
> others have somehow overcome this problem.
> 
> The subroutine that triggers this error is pasted below:
> 
> (based on "Beginning perl for Bioinformatics"  as I am trying to adapt an
> example in that book for my work)
> 
> 
> $fh = open_file($library);
> 
> $offset = tell($fh);
> 
> while( $record = get_next_record($fh) ) {
> 
> my $locus=( );
> 
> ($annotation, $dna) = get_annotation_and_dna($record);
> 
> $offset = tell($fh);
> 
> 
> 
>  # Extract the fields of the annotation
> %fields = parse_annotation($annotation);
> 
> 
> Sub-routine that triggers the error message:
> 
> 
> sub parse_annotation {
> 
>    my($annotation) = @_;
>    my(%results) = (  );
> 
>    while( $annotation =~ /^[A-Z].*\n(^\s.*\n)*/gm ) {
>        my $value = $&;
>        (my $key = $value) =~ s/^([A-Z]+).*/$1/s;
>        $results{$key} = $value;
>    }
> 
>    return %results;
> }
> 
> thanks,
> 
> -gopal
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