[Bioperl-l] BioPerl-network problem?

[Chris Fields]

On Jul 27, 2009, at 7:32 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

The segfault makes me wonder if it could have something to do with the  
XML parser.  Can you file this as a bug report so we can track it?

http://www.bioperl.org/wiki/Bugs
http://bugzilla.open-bio.org/

chris