Flashpoint avatar Flashpoint committed 3a530b6

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

Comments (0)

Files changed (4)

_bioinformatics/obiGeneSets.py

 
     return GeneSets(genesets)
 
+def cytobandGeneSets():
+    """
+    Return cytoband gene sets from Stanford Microarray Database
+    """
+    from . import obiCytobands
+    
+    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
+                        link="") \
+                        for band in obiCytobands.bands()]
+  
+    return GeneSets(genesets)
+
 def omimGeneSets():
     """
     Return gene sets from OMIM (Online Mendelian Inheritance in Man) diseses

_bioinformatics/obiOMIM.py

     """ Return a dictionary {gene: set(disease_objects for gene), ...}
     """
     return OMIM.get_instance().gene_diseases()
+
+if __name__ == "__main__":
+    print genes()

_bioinformatics/widgets/OWSetEnrichment.py

 
         dsp, dspcb = OWGUI.doubleSpin(hWidget, self,
                         "maxPValue", 0.0, 1.0, 0.0001,
-                        label="P-Value (FDR corrected)",
-                        tooltip="Maximum (FDR corrected) P-Value",
+                        label="FDR adjusted P-Value",
+                        tooltip="Maximum (FDR adjusted) P-Value",
                         callback=self.filterAnnotationsChartView,
                         callbackOnReturn=True,
                         checked="useMaxPValFilter",

server_update/updateOMIM.py

 ##!interval=7
 ##!contact=ales.erjavec@fri.uni-lj.si
 
+
 from common import *
 from Orange.bio import obiOMIM
 
 sf_server.upload("OMIM", "morbidmap", filename, title="Online Mendelian Inheritance in Man (OMIM)",
                    tags=["genes", "diseases", "human", "OMIM" "#version:%i" % obiOMIM.OMIM.VERSION])
 sf_server.unprotect("OMIM", "morbidmap")
+
+
+"""
+Orange server upload for OMIM morbidmap gene sets
+"""
+from Orange.bio.obiGeneSets import omimGeneSets, register
+
+omim_sets_split = omimGeneSets().split_by_hierarchy()
+for omim_sets in omim_sets_split:
+    register(omim_sets, sf_server)
+
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for ProjectModifiedEvent.java.
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.