-
-
-def buildScerevisiaeDB(db=geneDB):
- genePath = "%s/download/SGD_features.tab" % cisRoot
- goDefPath = "%s/download/GO.terms_and_ids" % cisRoot
- goPath = "%s/download/gene_association.sgd" % cisRoot
- chromos = {"1": "%s/download/chr01.fsa" % cisRoot,
- "2": "%s/download/chr02.fsa" % cisRoot,
- "3": "%s/download/chr03.fsa" % cisRoot,
- "4": "%s/download/chr04.fsa" % cisRoot,
- "5": "%s/download/chr05.fsa" % cisRoot,
- "6": "%s/download/chr06.fsa" % cisRoot,
- "7": "%s/download/chr07.fsa" % cisRoot,
- "8": "%s/download/chr08.fsa" % cisRoot,
- "9": "%s/download/chr09.fsa" % cisRoot,
- "10": "%s/download/chr10.fsa" % cisRoot,
- "11": "%s/download/chr11.fsa" % cisRoot,
- "12": "%s/download/chr12.fsa" % cisRoot,
- "13": "%s/download/chr13.fsa" % cisRoot,
- "14": "%s/download/chr14.fsa" % cisRoot,
- "15": "%s/download/chr15.fsa" % cisRoot,
- "16": "%s/download/chr16.fsa" % cisRoot
- }
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, genePath)
-
- print "Adding gene annotations"
- loadGeneAnnotations(db, genePath)
-
- print "Adding gene ontology"
- loadGeneOntology(db, goPath, goDefPath)
-
- for chromID in ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"]:
- print "Loading chromosome %s" % chromID
- loadChromosome(db, chromID, chromos[chromID], "/S_cerevisiae/chr%s.bin" % chromID)
-
- print "Creating Indices"
- createDBindices(db)
-
- print "Finished creating database %s" % db
\ No newline at end of file