[Bioperl-l] BioPerl-network problem?

[Brian Osborne]

Sirisha,

Yes, I've noticed this too and talk about it in the Wiki:

http://www.bioperl.org/wiki/Module:Bio::Graph::IO::psi_xml

Unfortunately there are different "flavors" of PSI MI 2.5, and I  
elected not to try to parse a flavor that either didn't match  
Bioperl's data model or that didn't precisely adhere to PSI MI. I've  
found that another reliable source of PSI 2.5 files is IntAct, try  
those files. Just a detail, the real error you're seeing is this:

> No fullName for interactor Aldehyde dehydrogenase 1


That tells you what the problem is although, as the Wiki page says,  
there may be other problems with files from HPRD.

Brian O.


On Jul 27, 2009, at 8:32 AM, Sirisha Gollapudi wrote:

> Hi everyone,
>
> I'm trying to use Bio::Network (version 1.6.0) to parse the file  
> "HPRD_SINGLE_PSIMI_070609.xml" which I've downloaded from the HPRD  
> website (http://www.hprd.org/download). This is the code I'm using:
>
> #!/usr/bin/perl -w
> use lib "/opt/bioperl_1.6.0/lib/perl5/";
> use Bio::Network::IO;
>
> use Getopt::Std;
> my %opts;
> getopts('i:', \%opts);
>
> my $input_file = $opts{i};
>
> my $io = Bio::Network::IO->new(-file => $input_file,
>                                 -format => 'psi25',
>                                 -verbose => 1 );
>
> my $network = $io->next_network;
>
>
> Which gives the following:
>
> No fullName for interactor Aldehyde dehydrogenase 1
> Use of uninitialized value in string eq at /opt/bioperl_1.6.0/lib/ 
> perl5//Bio/Network/IO/psi25.pm line 376.
> Use of uninitialized value in string eq at /opt/bioperl_1.6.0/lib/ 
> perl5//Bio/Network/IO/psi25.pm line 376.
> Use of uninitialized value in string eq at /opt/bioperl_1.6.0/lib/ 
> perl5//Bio/Network/IO/psi25.pm line 376.
> Use of uninitialized value in string eq at /opt/bioperl_1.6.0/lib/ 
> perl5//Bio/Network/IO/psi25.pm line 376.
> Use of uninitialized value in string eq at /opt/bioperl_1.6.0/lib/ 
> perl5//Bio/Network/IO/psi25.pm line 376.
> Use of uninitialized value in string eq at /opt/bioperl_1.6.0/lib/ 
> perl5//Bio/Network/IO/psi25.pm line 376.
> Segmentation fault
>
>
>
> I've tried with numerous other PSI-MI v2.5 files, and the only ones  
> that "work" are those from MINT - all the others give the same "Use  
> of uninitialized value" error as above. I've tried DIP, BioGRID and  
> MPact. Any advice on the errors would be great!
>
> Best wishes,
>
> Sirisha
>
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