-
-
-def buildCelegansDB(db=geneDB, downloadRoot=""):
- if downloadRoot == "":
- downloadRoot = "%s/download/" % cisRoot
-
- geneIDPath = "%sgeneIDs.WS200" % downloadRoot
- goDefPath = "%sGO.terms_and_ids" % downloadRoot
- goPath = "%sgene_association.wb" % downloadRoot
-
- # can be found at ftp://caltech.wormbase.org/pub/schwarz/cisreg/softmasks
- chromos = {"I": "%sCHROMOSOME_I_softmasked.dna" % downloadRoot,
- "II": "%sCHROMOSOME_II_softmasked.dna" % downloadRoot,
- "III": "%sCHROMOSOME_III_softmasked.dna" % downloadRoot,
- "IV": "%sCHROMOSOME_IV_softmasked.dna" % downloadRoot,
- "V": "%sCHROMOSOME_V_softmasked.dna" % downloadRoot,
- "X": "%sCHROMOSOME_X_softmasked.dna" % downloadRoot
- }
-
- # can be found at ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF2/elegansWS160.gff.gz
- gffPath = "%selegansWS200.gff" % downloadRoot
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, gffPath)
-
- print "Adding feature entries"
- loadFeatureEntries(db, gffPath)
-
- print "Adding gene annotations"
- loadGeneAnnotations(db, geneIDPath)
-
- print "Adding gene ontology"
- loadGeneOntology(db, goPath, goDefPath, geneIDPath)
-
- for chromID in chromos:
- print "Loading chromosome %s" % chromID
- loadChromosome(db, chromID, chromos[chromID], "/C_elegans/chr%s.bin" % chromID)
-
- print "Creating Indices"
- createDBindices(db)
-
- print "Finished creating database %s" % db
\ No newline at end of file