- atGenome.addChromosomeEntry(chromID, chromOut, "file")
- # Add alternative chromID - should be A-O and 01-09
- atGenome.addChromosomeEntry("chromo%s" % chromID, chromOut, "file")
+ print "Adding gene annotations"
+ loadGeneAnnotations(db, annotPath)
+
+ print "Adding gene ontology"
+ loadGeneOntology(db, goPath)
+
+ for chromID in ["1", "2", "3", "4", "5", "C", "M"]:
+ print "Loading chromosome %s" % chromID
+ chromPath = "%s/chr%s.fas" % (downloadDir, chromID)
+ loadChromosome(db, chromID, chromPath, "/A_thaliana/chr%s.bin" % chromID)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
+
+
+def createDBFile(db):
+ atGenome = Genome("athaliana", dbFile=db)
+ atGenome.createGeneDB(db)