default=False,
action="store_true",
help="Run in parallel mode")
return parser
if __name__ == '__main__':
parser = getOptions()
(options, args) = parser.parse_args()
if not options.dbname or not options.fasta_file:
parser.print_help()
sys.exit(1)
if not options.output_path:
options.output_path = options.dbname
if not os.path.exists(options.output_path):
os.mkdir(options.output_path)
if options.parallel:
options.parallel = pp.Server()
united = UnitiedDB(options.dbname + '.db')
meme_slv = shelve.open(options.dbname + ".slv")
meme_ids = loadMEME_ID(eval(options.subset, {}, {}))
meme_ids = list(set(united.getMEME_ID({})) & set(meme_ids))
print len(meme_ids), "to be scanned"
timestamp = time.time()
if options.parallel:
scanMotifsParallel(options, united, meme_slv, meme_ids)
else:
scanMotifs(options, united, meme_slv, meme_ids)
print time.time() - timestamp
parser.add_option("-c", "--plantcare", dest="plantcare", help="Import PlantCARE", default=False, action="store_true")
parser.add_option("-p", "--place", dest="place", help="Import PLACE", default=False, action="store_true")
parser.add_option("-d", "--denovo", dest="denovo_path", help="Import Denovo Motifs(MEME format only)", metavar="DIR")
(options, args) = parser.parse_args()
if not options.dbname:
parser.print_help()
sys.exit(1)
jaspar_path = './databases/jaspar.db'
plantcare_path = './databases/plantcare.db'
place_path = './databases/place.db'
meme_slv = shelve.open(options.dbname + ".slv")
united = UnitiedDB(options.dbname + ".db")
#initialize databases
if options.jaspar:
if not os.path.exists(jaspar_path):
jaspar = JasparDB(jaspar_path)
jaspar.importTables('./databases/jaspar/')
else:
jaspar = JasparDB(jaspar_path)
meme_motifs = jaspar2meme('./databases/jaspar_pfm/')
meme_slv.update(split_meme(meme_motifs))
united.importDB('Jaspar', jaspar_path)
if options.plantcare:
if not os.path.exists(plantcare_path):
plantcare = PlantCARE(plantcare_path)
plantcare.importMotifs('./databases/plantcare.txt')