#!/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')