def loadMEME_ID(subset):
care = PlantCARE('./databases/plantcare.db')
place = Place('./databases/place.db')
jaspar = JasparDB('./databases/jaspar.db')
meme_ids = []
print subset
if 'plantcare' in subset.keys() and subset['plantcare'] != None:
meme_ids.extend(care.getMotifSeq(subset['plantcare']))
if 'place' in subset.keys() and subset['place'] != None:
tmp_seq = place.getMotifSeq(subset['place'])
#for those contain U would change by iupac2meme to T
#causing KeyError
tmp_seq = [seq.replace("U", "T") for seq in tmp_seq]
meme_ids.extend(tmp_seq)
if 'jaspar' in subset.keys() and subset['jaspar'] != None:
meme_ids.extend(jaspar.getBASE_ID(subset['jaspar']))
if 'denovo' in subset.keys() and subset['denovo'] != None:
meme_ids.extend(united.getMEME_ID(subset['denovo']))
return list(set(meme_ids))
(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')
else:
plantcare = PlantCARE(plantcare_path)
meme_motifs = iupac2meme(plantcare.getMotifSeq())
meme_slv.update(split_meme(meme_motifs))
