maskRegion.py

#!/usr/bin/env python
import pybedtools
import pandas as pd

ps = pybedtools.BedTool(snakemake.input[0])
if '.pos.' in snakemake.input[0]:
    strand='+'
elif '.neg.' in snakemake.input[0]:
    strand='-'

if snakemake.params[0]=='':
    df=ps
else:   
    frame_mf=pd.read_csv(snakemake.params[0],delimiter='\t',header=None)
    frame_mf=frame_mf[frame_mf[5]==strand]
    mf = pybedtools.BedTool.from_dataframe(frame_mf)
    df = ps.subtract(mf)
df.moveto(snakemake.output[0])