[Bioperl-l] phd format parsing produces infinite memory usage

Jorge.DUARTE at biogemma.com Jorge.DUARTE at biogemma.com
Mon Jul 28 04:11:17 EDT 2008


bioperl-l-bounces at lists.open-bio.org a écrit sur 24/07/2008 23:38:33 :

> Jean-Marc FRIGERIO wrote:
> >
> > Huuh !! phd files should contain only one sequence !! 
> >
> >
> > 
> This is no longer necessarily true. Consed allows concatenated phd files 

> now.
> 

Alright,

thank you for your answers.

In case it can help others until the parser is updated,
if i modify the phd.pm code this way, it seems to work fine for my file :

        if ($entry =~ /^END_SEQUENCE/) {
                $entry = $self->_readline();
                last;
        }

I'm not sure this is the best way to do it though, as i'm not a perl 
expert.

Thanks for your help,
Jorge.


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