Changeset 1780:5cc362d703bb in orange-bioinformatics for _bioinformatics/obiGeneSets.py


Ignore:
Timestamp:
05/10/13 10:46:01 (11 months ago)
Author:
Flashpoint <vid.flashpoint@…>
Branch:
default
Message:

DictyMutants geneset working

File:
1 edited

Legend:

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  • _bioinformatics/obiGeneSets.py

    r1778 r1780  
    6666    """ 
    6767    from . import obiDictyMutants 
    68     genesets = [GeneSet(id=dicty_mutant.id, name=dicty_mutant.descriptor, genes=obiDictyMutants.mutant_genes(mutant), hierarchy=("Dictybase", "mutant_phenotypes"), organism="352472", # 352742 gathered from obiGO.py code_map -> Dicty identifier 
    69                         link=("http://dictybase.org/db/cgi-bin/dictyBase/SC/scsearch.pl?searchdb=strains&search_term=%s&column=all&B1=Submit" % mutant.id if mutant.id else None)) \ 
     68    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)) \ 
    7071                        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()]) 
     75 
    7176    return GeneSets(genesets) 
    7277 
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