support for HPRD PSI-MI 2.5 XML, was: Bioperl-network parsing error

[cjfields]

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Author Name: Sirisha Gollapudi (Sirisha Gollapudi) Original Redmine Issue: 2886, https://redmine.open-bio.org/issues/2886 Original Date: 2009-07-27 Original Assignee: Bioperl Guts

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I’m trying to use Bio::Network (version 1.6.0) to parse the PSI-MI v2.5 file “HPRD_SINGLE_PSIMI_070609.xml” which I’ve downloaded from the HPRD website (http://www.hprd.org/download).

The parsing script gives the following errors:

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. Other files I’ve tried are from DIP, BioGRID and MPact.

My Perl is v5.8.8 built for x86_64-linux-thread-multi.

[cjfields]

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Original Redmine Comment Author Name: Chris Fields Original Date: 2009-08-06T22:36:24Z

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Pushing this to a later release; for more details on a workaround, see:

http://www.bioperl.org/wiki/Module:Bio::Graph::IO::psi\_xml

[cjfields]

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Original Redmine Comment Author Name: Chris Fields Original Date: 2009-10-26T21:12:11Z

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Moving this to an enhancement request; problems with the XML from different sites has been noted in the module POD and on the bioperl wiki.