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

[Jason Stajich]

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/