lab03.py

f = open("Homo_sapiens.GRCh38.114.gtf", "r")
c = f.read().split("\n")
del c[0:4]
c.pop()

c = [s.split("\t") for s in c]
lengths = {}
i = 0
for l in c:
    try:
        if(l[2] == "gene"):
            lengths[i] = {
                "length": int(l[4]) - int(l[3]) + 1,
                "info": l
            }
        i += 1
    except:
        continue

lengths = sorted(lengths.items(),  key=lambda x: x[1]["length"], reverse=True)[:3]

print("top 3 longest:")
for l, data in lengths:
    info = data["info"]
    print(f"len: {data['length']}, gene_id: {info[8].split('gene_id \"')[1].split('\"')[0]}, gene_name: {info[8].split('gene_name \"')[1].split('\"')[0]}")


t = {}
for l in c:
    try:
        if l[2] == "transcript":
            gene_id = l[8].split('gene_id "')[1].split('"')[0]
            gene_name = l[8].split('gene_name "')
            if gene_id not in t:
                t[gene_id] = {"count": 1, "gene_name": gene_name}
            else:
                t[gene_id]["count"] += 1
    except:
        continue

transcripts = sorted(t.items(), key=lambda x: x[1]["count"], reverse=True)[:3]

print("top 3 with the most transcript count:")
for gene_id, data in transcripts:
    print(f"gene_id: {gene_id}, transcripts: {data['count']}")