Changeset 1794:3a530b619d7f in orange-bioinformatics


Ignore:
Timestamp:
05/20/13 09:17:21 (11 months ago)
Author:
Flashpoint <vid.flashpoint@…>
Branch:
default
Message:

Added Cytobands genesets and modified obiOMIM.py. Both need some extra work.

Files:
4 edited

Legend:

Unmodified
Added
Removed
  • _bioinformatics/obiGeneSets.py

    r1782 r1794  
    7575                        for phenotype, mutants in obiDictyMutants.phenotype_mutants().items()] 
    7676 
     77    return GeneSets(genesets) 
     78 
     79def cytobandGeneSets(): 
     80    """ 
     81    Return cytoband gene sets from Stanford Microarray Database 
     82    """ 
     83    from . import obiCytobands 
     84     
     85    genesets = [GeneSet(id=band.name, name=band.descriptor, genes=obiCytobands.band_genes(band), hierarchy=("Cytobands",), organism="9606", # 352472 gathered from obiGO.py code_map -> Dicty identifier 
     86                        link="") \ 
     87                        for band in obiCytobands.bands()] 
     88   
    7789    return GeneSets(genesets) 
    7890 
  • _bioinformatics/obiOMIM.py

    r1719 r1794  
    101101    """ 
    102102    return OMIM.get_instance().gene_diseases() 
     103 
     104if __name__ == "__main__": 
     105    print genes() 
  • _bioinformatics/widgets/OWSetEnrichment.py

    r1793 r1794  
    141141        dsp, dspcb = OWGUI.doubleSpin(hWidget, self, 
    142142                        "maxPValue", 0.0, 1.0, 0.0001, 
    143                         label="P-Value (FDR corrected)", 
    144                         tooltip="Maximum (FDR corrected) P-Value", 
     143                        label="FDR adjusted P-Value", 
     144                        tooltip="Maximum (FDR adjusted) P-Value", 
    145145                        callback=self.filterAnnotationsChartView, 
    146146                        callbackOnReturn=True, 
  • server_update/updateOMIM.py

    r1721 r1794  
    11##!interval=7 
    22##!contact=ales.erjavec@fri.uni-lj.si 
     3 
    34 
    45from common import * 
     
    1920                   tags=["genes", "diseases", "human", "OMIM" "#version:%i" % obiOMIM.OMIM.VERSION]) 
    2021sf_server.unprotect("OMIM", "morbidmap") 
     22 
     23 
     24""" 
     25Orange server upload for OMIM morbidmap gene sets 
     26""" 
     27from Orange.bio.obiGeneSets import omimGeneSets, register 
     28 
     29omim_sets_split = omimGeneSets().split_by_hierarchy() 
     30for omim_sets in omim_sets_split: 
     31    register(omim_sets, sf_server) 
     32 
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