def mergeFeatures(features): currChrom = features[0][0] currStart = features[0][1] currEnd = features[0][2] currStrand = features[0][5] merged= [] count = 1 for e in features: if e[5] == currStrand and currChrom == e[0] and fo.getOverlapOri(currStart,currEnd,e[1],e[2]) > 0: if e[2] > currEnd: currEnd = e[2] if e[1] < currStart: currStart = e[1] else: merged.append([currChrom,currStart,currEnd,count,0,currStrand]) currChrom = e[0] currStart = e[1] currEnd = e[2] currStrand = e[5] count += 1 merged.append([currChrom,currStart,currEnd,count,0,currStrand]) return merged
for r in reader:
transcripts.append(r)
transcripts.sort(key=lambda k: (k["name"], k["chrom"], int(k["chromStart"]), int(k["chromEnd"])))
genes = {}
for t in transcripts:
if t["name"] not in genes:
genes[t["name"]] = [[t["chrom"], t["chromStart"], t["chromEnd"], t["name"], t["score"], t["strand"]]]
else:
if t["chrom"] != genes[t["name"]][-1][0]:
genes[t["name"]].append([t["chrom"], t["chromStart"], t["chromEnd"], t["name"], t["score"], t["strand"]])
else:
if (
fo.getOverlapOri(
int(t["chromStart"]), int(t["chromEnd"]), int(genes[t["name"]][-1][1]), int(genes[t["name"]][-1][2])
)
> 0
):
if int(t["chromStart"]) < int(genes[t["name"]][-1][1]):
genes[t["name"]][-1][1] = t["chromStart"]
if int(t["chromEnd"]) > int(genes[t["name"]][-1][2]):
genes[t["name"]][-1][2] = t["chromEnd"]
else:
genes[t["name"]].append(
[t["chrom"], t["chromStart"], t["chromEnd"], t["name"], t["score"], t["strand"]]
)
records = []
out = open(sys.argv[2], "w")
for g in genes:
