import pandas as pd import sys, argparse, os # input arguments parser = argparse.ArgumentParser(description="This script is to get 1500bp surround SV breakpoint,") parser.add_argument('-SV', '--SV_bed_file', type=str, help='The SV breakpoint bed file', required=True) parser.add_argument('-prefix', '--prefix', type=str, help='The prefix of output file', required=True) args = parser.parse_args() SV = args.SV_bed_file prefix = args.prefix sv = pd.read_table(SV,header=None) # left for i in range(50,1550,50): sv.iloc[:,2] = sv.iloc[:,1] sv.iloc[:,1] = sv.iloc[:,1] - 50 file_name = prefix + '.' + str(i) + '.left.bed' sv.to_csv(file_name,sep="\t",index=0,header=None) sv = pd.read_table(SV,header=None) # right for i in range(50,1550,50): sv.iloc[:,1] = sv.iloc[:,2] sv.iloc[:,2] = sv.iloc[:,2] + 50 file_name = prefix + '.' + str(i) + '.right.bed' sv.to_csv(file_name,sep="\t",index=0,header=None)