Re: [GMOD-devel] Bio::Chaos::ChaosGraph.pm

[chris m. <cj...@fr...>]

I didn't realise Bio::Chaos shipped with gmod! The one on CPAN should  
be regarded as the stable, public one. I once kept Bio-Chaos in gmod/ 
chado cvs but it now has a separate home on my svn server. Is there  
any action I need to take here Scott, or is this fixed in the next  
release?


On Aug 9, 2006, at 3:29 PM, Barry Moore wrote:

> Chris and Scott,
>
> Ran across something that might be of interest to both of you.  It  
> appears that the version of ChaosGraph.pm that ships with gmod is  
> out of date.  This manifest itself on my system as follows:  cx- 
> genbank2chaos.pl works fine with BioChaos-0.02 installed.  cx- 
> genbank2chaos.pl fails when I install gmod.  BioChaos and gmod ship  
> with slightly different versions of cx-genbank2chaos.pl.  Both of  
> these scripts fail when using gmod's version of ChaosGraph.pm and  
> both work when using BioChaos' version of ChaosGraph.pm.  The  
> failure is actually in Graph.pm, but it doesn't look like gmod  
> ships it's own version of Graph.pm and a stack trace at the time of  
> failure implicates ChaosGraph.pm:
>
> $ = Graph::_attr02_123(undef, undef, undef, undef, undef, 'type',  
> 'XM_971089.1', 'EMBL/GenBank/ 
> SwissProt:exon:NW_001092775:2135464:2135680', 'XM_962777.1', 'EMBL/ 
> GenBank/SwissProt:exon:NW_001092775:2135464:2135680') called from  
> file `/usr/lib/perl5/site_perl/5.8.5/Graph.pm' line 2390
> $ = Graph::get_attribute(ref(Graph), 'type', 'XM_971089.1', 'EMBL/ 
> GenBank/SwissProt:exon:NW_001092775:2135464:2135680',  
> 'XM_962777.1', 'EMBL/GenBank/ 
> SwissProt:exon:NW_001092775:2135464:2135680') called from file `/ 
> usr/lib/perl5/site_perl/5.8.5/Bio/Chaos/ChaosGraph.pm' line 562
> $ = Bio::Chaos::ChaosGraph::feature_relationships_for_subject(ref 
> (Bio::Chaos::ChaosGraph), ref(Data::Stag::StagImpl)) called from  
> file `/usr/lib/perl5/site_perl/5.8.5/Bio/Chaos/ChaosGraph.pm' line 691
> $ = Bio::Chaos::ChaosGraph::make_island(ref 
> (Bio::Chaos::ChaosGraph), ref(Data::Stag::StagImpl), 500) called  
> from file `/usr/local/bin/cx-genbank2chaos.pl' line 138
> . = eval {...} called from file `/usr/local/bin/cx- 
> genbank2chaos.pl' line 135
>
> The error message from the script is:
>
> get_attribute: wrong number of arguments (5) at /usr/lib/perl5/ 
> site_perl/5.8.5/Graph.pm line 2346, <GEN0> line 65627.
> Problem resides with source feature
> <?xml version="1.0" encoding="UTF-8"?>
> <feature>
>   <feature_id>EMBL/GenBank/ 
> SwissProt:gene:NW_001092775:2133333:2136242</feature_id>
>   <name>LOC663447</name>
>   <uniquename>Tribolium_castaneum:LOC663447</uniquename>
>   <type>gene</type>
>   <organismstr>Tribolium castaneum (red flour beetle)</organismstr>
>   <featureloc>
>      
> <srcfeature_id>contig:GenericSeqDB:NW_001092775.1:2136742:2132832</ 
> srcfeature_id>
>     <nbeg>500</nbeg>
>     <nend>3410</nend>
>     <strand>-1</strand>
>     <rank>0</rank>
>   </featureloc>
>   <feature_dbxref>
>     <dbxrefstr>GeneID:663447</dbxrefstr>
>   </feature_dbxref>
>   <featureprop>
>     <type>db_xref</type>
>     <value>GeneID:663447</value>
>     <rank>0</rank>
>   </featureprop>
>   <featureprop>
>     <type>gene</type>
>     <value>LOC663447</value>
>     <rank>0</rank>
>   </featureprop>
>   <featureprop>
>     <type>note</type>
>     <value>Derived by automated computational analysis using gene  
> prediction method: GNOMON.</value>
>     <rank>0</rank>
>   </featureprop>
> </feature>
>
> Barry
>