SV_MIE/codescripts/get_flanking_region.py

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)