Changeset 1715:87468c6e6443 in orange-bioinformatics for _bioinformatics/obimiRNA.py


Ignore:
Timestamp:
08/30/12 15:19:40 (20 months ago)
Author:
markotoplak
Branch:
default
Message:

Removed use of the old obiKEGG module. Hacked a REST version for gene aliases in obiKEGG2.

File:
1 edited

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  • _bioinformatics/obimiRNA.py

    r1713 r1715  
    77import statc 
    88 
    9 from . import obiGene as ge, obiGO as go, obiKEGG as kg, obiProb as op, obiTaxonomy 
     9from . import obiGene as ge, obiGO as go, obiKEGG2 as kg, obiProb as op, obiTaxonomy 
    1010 
    1111mirnafile = osf.localpath_download('miRNA','miRNA.txt') 
     
    407407        kegg_genes = [keggNames[g] for g in get_info(m).targets.split(',') if g in keggNames] 
    408408        if enrichment: 
    409             mirnaPathways[m] = [path_id for path_id,(geneList,p,geneNum) in org.get_enriched_pathways_by_genes(kegg_genes).items() if p < pVal] 
     409            mirnaPathways[m] = [path_id for path_id,(geneList,p,geneNum) in org.get_enriched_pathways(kegg_genes).items() if p < pVal] 
    410410        else: 
    411411            paths = filter(None,[list(org.get_pathways_by_genes([k])) for k in kegg_genes])                    
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