[Bioperl-l] AlignIO crashes when reading stockholm alignment with negative PDB ranges

[Jason Stajich]

Alexandr -

Thanks for getting back to us - I am guessing the parser needs to  
recognize negative coordinates around about line 370 in Bio/AlignIO/ 
Handler/GenericAlignHandler.pm which assumes a split on '-' will be  
sufficient.

Can you post it as a bug to bugzilla along with attaching a record and  
script that replicates the problem so a test can be written for this. http://bugzilla.open-bio.org/

-jason
On Jan 18, 2010, at 4:54 PM, Alexandr Bezginov wrote:

> I have contacted Pfam, and I have been told that The PDB file actually
> does include a reference to residue "-1":
>
> DBREF  1E5N A   -1   347  UNP    P14768   XYNA_PSEFL     264    611
>
> DBREF  1E5N B   -1   347  UNP    P14768   XYNA_PSEFL     264    611
>
>
> Since negative numbers are allowed in PDB, the data should probably be
> considered valid.
>
> There are quite a few records like this, so this is not an isolated  
> issue.
>
> Alexandr
>
> On 1/14/2010 7:20 PM, Jason Stajich wrote:
>> Seems like improper data really -- "-1" is an improper coordinate  
>> as far
>> as the parser is concerned. You may want to tell Pfam that there is
>> possible error in the dumper since that was the only record that had
>> this problem?
>>
>> -jason
>> On Jan 13, 2010, at 5:57 PM, albezg wrote:
>>
>>> Hi all,
>>>
>>> I have a problem using AlignIO to read Pfam database:
>>> ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.seed.gz
>>> The database is in STOCKHOLM 1.0 format. AlignIO can read the
>>> alignment OK until the alignment PF00331.13. There it crashes with  
>>> the
>>> following message:
>>>
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: '1-344' is not an integer.
>>>
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw
>>> /home/albezg/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:368
>>> STACK: Bio::Range::end
>>> /home/albezg/lib/perl5/site_perl/5.10.0/Bio/Range.pm:228
>>> STACK: Bio::Annotation::Target::new
>>> /home/albezg/lib/perl5/site_perl/5.10.0/Bio/Annotation/Target.pm:82
>>> STACK: Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target
>>> /home/albezg/lib/perl5/site_perl/5.10.0/Bio/AlignIO/Handler/ 
>>> GenericAlignHandler.pm:293
>>>
>>> STACK: Bio::AlignIO::Handler::GenericAlignHandler::data_handler
>>> /home/albezg/lib/perl5/site_perl/5.10.0/Bio/AlignIO/Handler/ 
>>> GenericAlignHandler.pm:73
>>>
>>> STACK: Bio::AlignIO::stockholm::next_aln
>>> /home/albezg/lib/perl5/site_perl/5.10.0/Bio/AlignIO/stockholm.pm:471
>>> STACK: /home/albezg/scripts/pfam2fasta.pl:22
>>> -----------------------------------------------------------
>>>
>>> It appears this is caused by this entry:
>>> #=GS XYNA_PSEFL/263-608    DR PDB; 1e5n B; -1-344;
>>>
>>> I don't care about residues in PDB, so I have just removed minus  
>>> signs
>>> from the ranges. This seems to have fixed the crashing.
>>>
>>> Is it a known problem? Is there a solution for it?
>>>
>>> Thanks,
>>> Alexandr
>>>
>>>
>>> On 03/20/2009 05:09 PM, albezg wrote:
>>>>
>>>> I'm trying to change FASTA header(display_id) for a sequence in an
>>>> alignment(SimpleAlign).
>>>>
>>>> There are no issues when I print it, however when I use AlignIO  
>>>> to write
>>>> the alignment to a FASTA file, it does not work. Is this behavior
>>>> intended?
>>>>
>>>> Demo code: http://github.com/jhannah/sandbox/tree/master/Bio_AlignIO_bug
>>>>
>>>> The error:
>>>> ------------- EXCEPTION -------------
>>>> MSG: No sequence with name [1/1-11]
>>>> STACK Bio::SimpleAlign::displayname
>>>> /scratch/BioSoftware/bioperl-live/Bio/SimpleAlign.pm:2659
>>>> STACK Bio::AlignIO::fasta::write_aln
>>>> /scratch/BioSoftware/bioperl-live/Bio/AlignIO/fasta.pm:200
>>>> STACK toplevel ./demo.pl:14
>>>> -------------------------------------
>>>>
>>>> Alexandr
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> http://fungalgenomes.org/
>>
>

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/