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

Chris Fields cjfields at illinois.edu
Mon Jan 18 21:19:30 EST 2010


Alexandr,

Posting the bug report would be great, should be an easy enough fix.

chris

On Jan 18, 2010, at 7:04 PM, Jason Stajich wrote:

> 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/
> 
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