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Flashpoint committed 7187e6b

Added some missing info to the obiGeneAtlas.py API

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  • Parent commits 4c6214c

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Files changed (3)

_bioinformatics/obiGeneAtlas.py

                      description="Diff. expressed in %s=%s" % (ef_display, efv),
                      link="http://www.ebi.ac.uk/gxa/qrs?specie_0={organism}&gprop_0=&gnot_0=&gval_0=&fact_1=&fexp_1=UPDOWN&fmex_1=&fval_1=%22{efv}%22+&view=hm".format( \
                             organism=organism, efv="+".join(efv.lower().split())),
-                     hierarchy=("Tissues", ef_display))
+                     hierarchy=("Gene expression atlas", ef_display))
         gene_sets.append(gs)
     return GeneSets(gene_sets)
 
         url += "&format={0}".format(format)
         if indent:
             url += "&indent"
-#        print url
+        #print url
+
         if self.cache is not None:
             return self._query_cached(url, format)
         else:
 ATLAS_ORGANISMS = \
     ["Anopheles gambiae",
      "Arabidopsis thaliana",
+     "Bacillus subtilis",
      "Bos taurus",
      "Caenorhabditis elegans",
+     "Canis familiaris",
+     "Ciona intestinalis",
+     "Ciona savignyi",
      "Danio rerio",
+     "Dasypus novemcinctus",
      "Drosophila melanogaster",
      "Epstein barr virus",
+     "Equus caballus",
      "Gallus gallus",
+     "Gorilla gorilla",
      "Homo sapiens",
      "Human cytomegalovirus",
+     "Human immunodeficiency virus",
      "Kaposi sarcoma-associated herpesvirus",
+     "Macaca mulatta",
+     "Monodelphis domestica",
      "Mus musculus",
+     "Ornithorhynchus anatinus",
+     "Oryza sativa",
+     "Pan troglodytes",
+     "Pongo abelii",
+     "Populus trichocarpa",
      "Rattus norvegicus",
      "Saccharomyces cerevisiae",
      "Schizosaccharomyces pombe",
-#     "Unknown",
-     "Xenopus laevis"
+     "Sus scrofa",
+     "Unknown",
+     "Vitis vinifera",
+     "Xenopus laevis",
+     "Xenopus tropicalis"
      ]
     
 def ef_ontology():
     def validate(self):
         # TODO: validate the factor and value
 #        assert(self.factor in ef_ontology())
-        assert(self.regulation in ["up", "down", "updown"])
+        assert(self.regulation in ["up", "down", "updown", "none", "any"])
         
     def rest(self):
         return "{regulation}{n}In{factor}={value}".format(**self.__dict__)
     
     :param genes: A list of gene names to search for.
     :param regulation: Search for experiments in which `genes` are "up",
-        "down", "updown" or "none" regulated. If None all experiments
+        "down", "updown", "any" or "none" regulated. If "any" all experiments
         are searched.
     :param organism: Search experiments for organism. If None all experiments
         are searched.

_bioinformatics/obiGeneSets.py

 def _register_local(genesets):
     """ Registers using the common hierarchy and organism. """
     pth = local_path()
-
     org = genesets.common_org()
     hierarchy = genesets.common_hierarchy()
     fn = filename(hierarchy, org)

_bioinformatics/widgets/OWSetEnrichment.py

 
         self.connect(self.groupsWidget, SIGNAL("itemClicked(QTreeWidgetItem *, int)"), self.subsetSelectionChanged)
 
+        self.omnibox = 1                                                                  ## A FUNCTION CALL TO HANDLE SELECTING/DESELECTING gene sets
+        OWGUI.checkBox(self.controlArea, self, "omnibox", "Select/Unselect all gene sets")#, callback= lambda :self.allSetsChanged())
+
         OWGUI.button(self.controlArea, self, "Commit", callback=self.commit)
 
         self.loadedGenematcher = "None"
         collection[taxid].update(collection[None])
         return collection[taxid]
 
+
+
+
+## AN ATTEMPT TO ENABLE/DISABLE all gene sets at once
+#    def allSetsChanged(self):
+#        print self.omnibox
+#        print self.getHierarchyCheckState()
+#        print self.categoriesCheckState
+#        print self.selectedCategories()
+        
+
+
     def setHierarchy(self, hierarchy):
         self.groupsWidgetItems = {}
         def fill(col, parent, full=()):
 
 
 
-if __name__ == "__main__":
+if __name__ == "__main__":  
     import cProfile
 
     app = QApplication(sys.argv)