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

[Alexandr Bezginov]

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