#!/usr/bin/env python

# -*- coding: utf-8 -*-

import argparse

import pyBigWig

from multiprocessing import Pool

from glob import glob

import os

import gzip

import numpy as np

import pandas as pd

import matplotlib.pyplot as plt

from singlecellmultiomics.methylation import sort_methylation_tabfile, methylation_tabfile_to_bed

from singlecellmultiomics.utils import create_fasta_dict_file

if __name__ == '__main__':

    argparser = argparse.ArgumentParser(

        formatter_class=argparse.ArgumentDefaultsHelpFormatter,

        description='Convert methylation calls from TAPS-tabulator to a methylation (big)bed file')

    argparser.add_argument('tabulated_file', type=str)

    argparser.add_argument(

        '-ref',

        type=str,

        help='path to reference fasta file, only required for bigbed files')

    argparser.add_argument(

        '--force-sort',

        action='store_true',

        help='Perform sort even when .sorted.gz already exists')

    argparser.add_argument(

        '-o',

        type=str,

        help='Output path, ends in .bed to get a bed file and .bb to get a compressed bigbed file')

    args = argparser.parse_args()

    tabulated_file = args.tabulated_file

    # First we need to sort the callfile

    if tabulated_file.endswith('.sorted.gz') and not args.force_sort:

        print('Input is sorted')

    else:

        if  args.force_sort:

            print("Performing sort")

        else:

            print("Input seems not to be sorted. Performing sort")

        pathout = tabulated_file + '.sorted.gz'

        sort_methylation_tabfile(tabulated_file, pathout)

        tabulated_file = pathout

    if args.o.endswith('.bb'):

        print('exporting to big-bed file')

        if args.ref is None:

            raise ValueError('-ref is required for bigbed output')

        dict_path = create_fasta_dict_file(args.ref)

        # We need to write the bed file temporarily

        output_path = args.o.replace('.bb','.bed')

        methylation_tabfile_to_bed(tabulated_file, output_path, invert_strand=True)

        # Perform bigbed conversion:

        os.system(f'bedToBigBed {output_path} {dict_path} {args.o} -type=bed8+3')

        if os.path.exists(args.o):

            os.remove(output_path)

            print('Completed')

        else:

            print('bedToBigBed failed, is bedToBigBed installed ?')

    else:

        print('exporting to bed file')

        output_path = args.o

        methylation_tabfile_to_bed(tabulated_file, args.o,  invert_strand=True)