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

Chris Fields cjfields at uiuc.edu
Mon Jul 28 11:59:57 EDT 2008


On Jul 28, 2008, at 3:11 AM, Jorge.DUARTE at biogemma.com wrote:

> 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.

We can add this in.  I'll add a few tests for multiple phd files to  
make sure it returns two Bio::Seq objects.

chris




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