Changeset 1781:764dc2b10839 in orange-bioinformatics for _bioinformatics/obiGeneSets.py


Ignore:
Timestamp:
05/10/13 15:19:06 (12 months ago)
Author:
Flashpoint <vid.flashpoint@…>
Branch:
default
Message:

First attempt at configuring Orange server update

File:
1 edited

Legend:

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  • _bioinformatics/obiGeneSets.py

    r1780 r1781  
    6767    from . import obiDictyMutants 
    6868    link_fmt = "http://dictybase.org/db/cgi-bin/dictyBase/SC/scsearch.pl?searchdb=strains&search_term=%s&column=all&B1=Submit"  
    69     genesets = [GeneSet(id=mutant.name, name=mutant.descriptor, genes=obiDictyMutants.mutant_genes(mutant), hierarchy=("Dictybase", ), organism="352472", # 352472 gathered from obiGO.py code_map -> Dicty identifier 
    70                         link=(link_fmt % mutant.name if mutant.name else None)) \ 
    71                         for mutant in obiDictyMutants.mutants()] 
    72     genesets.extend([GeneSet(id=mutant.name, name=mutant.descriptor, genes=obiDictyMutants.mutant_phenotypes(mutant), hierarchy=("Dictybase", "phenotype_mutants"), organism="352472", 
    73                         link=(link_fmt % mutant.name if mutant.name else None)) \ 
    74                         for mutant in obiDictyMutants.mutants()]) 
     69    #genesets = [GeneSet(id=mutant.name, name=mutant.descriptor, genes=obiDictyMutants.mutant_genes(mutant), hierarchy=("Dictybase", ), organism="352472", # 352472 gathered from obiGO.py code_map -> Dicty identifier 
     70    #                    link=(link_fmt % mutant.name if mutant.name else None)) \ 
     71    #                    for mutant in obiDictyMutants.mutants()] 
     72  
     73    genesets = [GeneSet(id=phenotype, name=phenotype, genes=[obiDictyMutants.mutant_genes(mutant)[0] for mutant in mutants], hierarchy=("Dictybase", ), organism="352472", # 352472 gathered from obiGO.py code_map -> Dicty identifier 
     74                        link="") \ 
     75                        for phenotype, mutants in obiDictyMutants.phenotype_mutants().items()] 
    7576 
    7677    return GeneSets(genesets) 
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