[Bioperl-l] problems with Bio::Graph

[Neil Saunders]

dear all,

I am having some problems with the Bio::Graph modules.  Running Bioperl 1.5.0 
RC1 with Ubuntu 5.10 i686.

I would like to parse files in PSI MI XML 2.5 format and for selected proteins, 
get the Uniprot accession of interacting partners (this is outlined in the 
documentation for Bio::Graph::ProteinGraph).  I wrote a very simple test script 
and ran it on a selection of XML files.  The script is simply:

----------------------------------------------------------------
use strict;
use Bio::Graph::IO;

my $mifile = shift || die("Usage = biograph.pl <MI datafile>\n");
my $graphio = Bio::Graph::IO->new('-file'   => $mifile,
		  		  '-format' => 'psi_xml');
my $gr = $graphio->next_network;
----------------------------------------------------------------

Here's a summary of the error messages with some sample files (I tried PSI MI 
XML versions 1 and 2.5):

1.  MINT database 9707552_small.xml (PSI 2.5)
Can't call method "att" on an undefined value at 
/usr/local/share/perl/5.8.7/Bio/Graph/IO/psi_xml.pm line 173.

2. IntAct database yeast_small-11.xml (PSI 2.5)
Can't call method "att" on an undefined value at 
/usr/local/share/perl/5.8.7/Bio/Graph/IO/psi_xml.pm line 173.

3. IntAct database yeast_small-11.xml (PSI 1)
Use of uninitialized value in string eq at 
/usr/local/share/perl/5.8.7/Bio/Graph/IO/psi_xml.pm line 126.

4. DIP files Scere20060402.mif, Ecoli20060402.mif (PSI 1)
These give no errors

5. DIP file dip20060402.mif (PSI 1, complete dataset)
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Invalid species name 'immunodeficiency virus type 1, HIV-1'
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.8.7/Bio/Root/Root.pm:328
STACK: Bio::Species::validate_species_name 
/usr/local/share/perl/5.8.7/Bio/Species.pm:340
STACK: Bio::Species::classification /usr/local/share/perl/5.8.7/Bio/Species.pm:170
STACK: Bio::Species::new /usr/local/share/perl/5.8.7/Bio/Species.pm:118
STACK: Bio::Graph::IO::psi_xml::_proteinInteractor 
/usr/local/share/perl/5.8.7/Bio/Graph/IO/psi_xml.pm:105
STACK: XML::Twig::_twig_end /usr/share/perl5/XML/Twig.pm:1473
STACK: XML::Parser::Expat::parse /usr/lib/perl5/XML/Parser/Expat.pm:469
STACK: XML::Parser::parse /usr/lib/perl5/XML/Parser.pm:187
STACK: XML::Parser::parsefile /usr/lib/perl5/XML/Parser.pm:233
STACK: Bio::Graph::IO::psi_xml::next_network 
/usr/local/share/perl/5.8.7/Bio/Graph/IO/psi_xml.pm:79
STACK: ./biograph.pl:18
-----------------------------------------------------------


Looking at the module code, it seems that the first 2 errors relate to a 
parameter "proteinInteractorRef", found in PSI MI version 1 but not version 2.5. 
  Error 3 I haven't yet figured out.  DIP PSI MI XML version 1 for single 
species seems OK, but it seems there are species names in the complete dataset 
that cause problems (error 5).


Is the CVS version of Bio::Graph any better at handling PSI MI XML?  Are there 
plans to get it to work with version 2.5 files from all sources (MINT and 
IntAct) ?  Googling and checking the list archives didn't give a lot of hits 
which made me think it's not a widely-used module.

thanks,
Neil
-- 
  School of Molecular and Microbial Sciences
  University of Queensland
  Brisbane 4072 Australia

http://psychro.bioinformatics.unsw.edu.au/neil