FilterMain.py

#!/usr/bin/env python

# encoding: utf-8

'''

@author: Jiadong Lin

@contact: jiadong324@gmail.com

@time: 2022/1/10
'''
import sys
import argparse
import os

from FilterRG import run_filter_region_graph
from FilterRep import run_filter_rep


def main():

    ## Filtering for the results in the paper
    # svision_vcf = '/Users/jiadonglin/SVision/HG00733/svision/v136/HG00733_docker_test.svision.s5.graph.vcf'
    # svision_exact_graph = '/Users/jiadonglin/SVision/HG00733/svision/v136/HG00733_docker_test.graph_exactly_match.txt'
    # outdir = '/Users/jiadonglin/SVision/HG00733/svision/v136'
    # exclude_graphid = ['0', '3']

    arguments = sys.argv[1:]

    parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
                                     description="""Support functions for SVision downstream analysis""")

    required_params = parser.add_argument_group("Input/Output parameters")
    required_params.add_argument('-v', dest="vcf", type=os.path.abspath, required=True,
                                 help='VCF file generated by SVision')
    required_params.add_argument('-g', dest="graph", type=os.path.abspath, required=True,
                                 help='Isomorphic graph file generated by SVision')
    required_params.add_argument('-w', dest='workdir', type=str, required=True,
                                 help='Absolute path to the work directory containing the VCF file')
    required_params.add_argument('-i', dest="id", type=str, required=True,
                                 help='Comma separated graph structures to excluded (e.g., 0,3)')

    optional_params = parser.add_argument_group("Optional parameters")
    optional_params.add_argument('-s', dest='min_sr', type=int, default=5, help='Minimum support read')
    optional_params.add_argument('-m', dest='max_sv_size', type=int, default=100000, help='Maximum SV size')

    options = parser.parse_args(arguments)

    svision_vcf = options.vcf
    svision_exact_graph = options.graph
    outdir = options.workdir
    exclude_graphid = options.id.split(',')
    min_sr = options.min_sr
    max_sv_size = options.max_sv_size

    print('===== Step 1 filter CSVs by region and graph structures =====')
    run_filter_region_graph(svision_vcf, svision_exact_graph, exclude_graphid, min_sr, max_sv_size, outdir)

    print('===== Step2 filter CSVs by simple repeats =====')
    run_filter_rep(outdir, svision_vcf)


if __name__ == '__main__':
    main()