#!/usr/bin/env python3

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

from singlecellmultiomics.statistic import PlateStatistic

import singlecellmultiomics.modularDemultiplexer

import math

import string

import pandas as pd

import matplotlib.pyplot as plt

import numpy as np

import os

import sys

import pysam

import collections

import argparse

from singlecellmultiomics.tagtools import tagtools

import pysamiterators.iterators as pysamIterators

import gzip

import pickle

import subprocess

import matplotlib

import matplotlib.lines as mlines

matplotlib.rcParams['figure.dpi'] = 160

matplotlib.use('Agg')

TagDefinitions = singlecellmultiomics.modularDemultiplexer.TagDefinitions

if __name__ == '__main__':

    argparser = argparse.ArgumentParser(

        formatter_class=argparse.ArgumentDefaultsHelpFormatter,

        description='Visualize single cell statistics on a plate plot')

    argparser.add_argument(

        '-o',

        type=str,

        help="output plot folder path, every library will be visualised as a separate plate",

        default='./plots/')

    argparser.add_argument('alignmentfiles', type=str, nargs='*')

    args = argparser.parse_args()

    if not os.path.exists(args.o):

        os.makedirs(args.o)

    ps = PlateStatistic(args)

    for alignmentFile in args.alignmentfiles:

        with pysam.AlignmentFile(alignmentFile) as f:

            for read in f:

                ps.processRead(read)

    ps.plot(args.o + '/PS')