[Bioperl-l] AlignIO crashes when reading stockholm alignment with negative PDB ranges
albezg
albezg at gmail.com
Thu Jan 14 01:57:27 UTC 2010
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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