File: gencode.py

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python-ncls 0.0.63-hotfix%2Bds-2
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import pandas as pd
from ncls import NCLS

d = pd.read_table("../gencode.v28.annotation.gtf.gz", usecols=[0, 3, 4], header=None, comment="#", names="Chromosome Start End".split(),  dtype={"Chromosome": "category"})

d = d[d.Chromosome == "chr1"]

n = NCLS(d.Start.values, d.End.values, d.index.values)

print(n)