Ejemplo n.º 1
0
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))
Ejemplo n.º 2
0
    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))
    united.importDB('PlantCARE', plantcare_path)

if options.place:
    if not os.path.exists(place_path):
        place = Place(place_path)
        place.importTable('./databases/place.tab')
    else:
        place = Place(place_path)
    meme_motifs = iupac2meme(place.getMotifSeq())
    meme_slv.update(split_meme(meme_motifs))
    united.importDB('PLACE', place_path)

if options.denovo_path:
    meme_motifs = open(options.denovo_path).read()
    meme_slv.update(split_meme(meme_motifs))
    united.importDenovo(options.denovo_path, 'MEME')