def predict_json(json_in, json_out):
"""
predict the splicing effect with Houdayer method
"""
json_splice = JsonSplice(json_in)
results = {}
for counter in range(0, len(json_splice.json_dict)): # len(json_splice.json_dict)
db_entry = json_splice.json_dict[counter]
chrom = db_entry["chrom"]
pos = db_entry["pos"]
alt = db_entry["alt"]
ref = db_entry["ref"]
ID = db_entry["ID"]
predict = SplicePredict(chrom, int(pos), ref, alt)
predict.ID = ID
predict.strategy = "Houdayer"
# predict.load_json(json_splice)
predict.score_annotate()
effect, comments = predict.predict()
print "[%s] chr%s:%s%s>%s : %s (%s)" % (ID, chrom, pos, ref, alt, ", ".join(effect), ", ".join(comments))
results[ID] = {"effect": effect, "comments": comments}
with open(json_out, "w") as f:
data = json.dumps(results, sort_keys=True, indent=4, separators=(",", ": "), ensure_ascii=True)
data = unicode(data.strip(codecs.BOM_UTF8), "utf-8")
f.write(data)
def predict_json(json_in, json_out, strategy = 'Houdayer'):
'''
predict the splicing effect
'''
print '***** PREDICTING *****'
db1 = json.loads(open(json_in, 'r').read())
records = list()
for record in db1:
p = SplicePredict(record)
p.set_ref_seq_gene(REFSEQGENE)
p.set_ref_seq(REFSEQ)
p.strategy = strategy
p.predict()
records.append(p)
with open(json_out, 'w') as f:
f.write(json.dumps(records, indent=4, ensure_ascii=False))