def diff(old, new, workdir=".gbdiff"):
print mkjs({"type": "diff", "source": old.name, "target": new.name})
oldrec = nebgb.parse(old).next()
oldrec.load_sequence()
newrec = nebgb.parse(new).next()
newrec.load_sequence()
seq_updated = update_features(oldrec, newrec, workdir)
for m in meta.diff(oldrec, newrec):
print mkjs(m)
(matched, todel, toins) = merge.merge(oldrec, newrec, seq_updated)
for td in todel:
print mkfeat(oldrec, td, delete=True)
for m in matched:
h1, h2 = map(mkjshash, m)
if h1 != h2:
m[0]["location"]["source"] = newrec.locus["source"]
print mkfeat(newrec, m[1], prev=m[0])
for ti in toins:
print mkfeat(newrec, ti)
def insert(handle):
print mkjs({"type": "insert", "source": handle.name})
rec = nebgb.parse(handle).next()
rec.load_sequence()
seqid = writeseq(rec.sequence)
rec.locus["source"] = seqid
print mkjs({"type": "keyword", "keyword": "locus", "value": rec.locus})
for kw in rec.keywords:
if kw == "reference":
for ref in rec.keywords[kw]:
print mkjs({
"type": "reference",
"refid": mkjshash(ref),
"value": ref
})
else:
print mkjs({
"type": "keyword",
"keyword": kw,
"value": rec.keywords[kw]
})
for f in rec.features:
print mkfeat(rec, f)