| Subject: | XRef parser does not load multiple cross-ref associations related to a same GO term |
| Date: | Mon, 27 May 2013 15:16:33 +0000 |
| To: | "bug-go-perl [...] rt.cpan.org" <bug-go-perl [...] rt.cpan.org> |
| From: | "Guignon, Valentin (Bioversity-France)" <v.guignon [...] cgiar.org> |
Hello,
after using the GO::Parser to load interpro2go cross-references, we noticed a sever bug: only one IPR could be associated to a single GO term!
I had a quick look into the Perl GO modules but I don't have enough time to get deeper to solve the bug (sorry). I just noticed that each time the parser meets a GO term, it creates a new instance for that term, discarding any other previous instance created for that term.
To help you a little, I added the appropriate additional tests to run to the test file "t150xref.t" (attached).
System info:
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Perl v5.8.8 built for x86_64-linux-thread-multi
# $Id: Parser.pm,v 1.15 2006/04/20 22:48:23 cmungall Exp $
# $Id: ObjCache.pm,v 1.3 2005/05/20 18:46:57 cmungall Exp $
# $Id: base_parser.pm,v 1.18 2008/03/13 05:16:40 cmungall Exp $
# $Id: go_xref_parser.pm,v 1.9 2010/02/15 17:34:57 cmungall Exp $
Linux 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
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I appreciate your time,
Valentin Guignon
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