def computeIntervalsBED(padding=25000, cutoff=0.9999): path = utl.outpath + 'real/HMM/h50.COMALE.df' df = pd.read_pickle(path) df = df[df.COMALE > df.COMALENC.quantile(cutoff)].COMALE.reset_index() df['start'] = df.POS - padding df['end'] = df.POS + padding df['name'] = '.' df = df[['CHROM', 'start', 'end', 'name', 'COMALE']] df = utl.mergeIntervals(df) df df.to_csv(utl.outpath + 'real/intervals.bed', sep='\t', header=None, index=None) df['len'] = df.end - df.start df.to_pickle(utl.outpath + 'real/intervals.df')