Changeset 1735:50499d1dc55a in orange-bioinformatics for _bioinformatics/obiGene.py


Ignore:
Timestamp:
04/05/13 19:43:32 (13 months ago)
Author:
Ales Erjavec <ales.erjavec@…>
Branch:
default
Message:

Changed the Organism.gene_aliases method.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • _bioinformatics/obiGene.py

    r1716 r1735  
    644644        self.filename() # test if valid filename can be built 
    645645 
    646 from Orange.utils import ConsoleProgressBar 
    647646 
    648647class MatcherAliasesKEGG(MatcherAliasesPickled): 
     
    652651 
    653652    def create_aliases(self): 
    654         organism = self._organism_name(self.organism) 
    655653        org = obiKEGG.KEGGOrganism(self.organism, genematcher=GMDirect()) 
    656         osets = org._gm_gene_aliases() 
     654        osets = org.gene_aliases() 
    657655        return osets 
    658656 
    659657    def create_aliases_version(self): 
    660         return obiKEGG.KEGGOrganism.organism_version(self.organism) + ".1" 
     658        # use KEGG short release string (e.g. '66.0+') 
     659        release = obiKEGG.KEGGOrganism.organism_version(self.organism) + ".2" 
     660        release, _ = release.split("/") 
     661        return release 
    661662 
    662663    def filename(self): 
    663         return "kegg_2_" + self._organism_name(self.organism)  
     664        return "kegg_2_" + self._organism_name(self.organism) 
    664665 
    665666    def __init__(self, organism, ignore_case=True): 
    666667        self.organism = organism 
    667668        MatcherAliasesPickled.__init__(self, ignore_case=ignore_case) 
     669 
    668670 
    669671class MatcherAliasesFile(MatcherAliasesPickled): 
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