#!/usr/bin/env python3

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

import os

import sys

import collections

import argparse

import singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods

from singlecellmultiomics.fastqProcessing.fastqIterator import FastqIterator

if __name__ == '__main__':

    argparser = argparse.ArgumentParser(

        formatter_class=argparse.ArgumentDefaultsHelpFormatter,

        description="""Extract features from a demultiplexed fastq file.

     Example usage: -seqfeatures BC,RX,SEQ -qualityfeatures QT,RQ,QUAL | gzip > bc_umi.fastq.gz

     """)  # -o ./bc_umi.fastq.gz

    argparser.add_argument(

        '-seqfeatures',

        type=str,

        help="Features to put into the ",

        required=True)

    argparser.add_argument(

        '-qualityfeatures',

        type=str,

        help="Features to put into ",

        required=True)

    argparser.add_argument(

        'fastqfiles',

        nargs='*',

        type=str,

        help="Input demultiplexed fastq files")

    argparser.add_argument('-format', type=str, help="Output format: fq, tsv")

    #argparser.add_argument('-o',  type=str, help="output file path", required=True)

    args = argparser.parse_args()

    seqfeatures = args.seqfeatures.split(',')

    qualityfeatures = args.qualityfeatures.split(',')

    if len(seqfeatures) != len(qualityfeatures):

        raise ValueError('Supply a quality feature for every sequence feature')

    TagDefinitions = singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TagDefinitions

    for reads in FastqIterator(*args.fastqfiles):

        for readIndex, record in enumerate(reads):

            tr = singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord(

                TagDefinitions)

            tr.fromTaggedFastq(record)

            sequence = ''.join(

                (record.sequence if tag == 'SEQ' else tr.tags.get(tag) for tag in seqfeatures))

            qualities = ''.join(

                (record.qual if tag == 'QUAL' else tr.tags.get(tag) for tag in qualityfeatures))

            if len(sequence) != len(qualities):

                raise ValueError(

                    'Length of base qualities does not match the length of the selected sequence features')

            if args.format == 'fq':

                print(f'{record.header}\n{sequence}\n+\n{qualities}')

            elif args.format == 'tsv':

                print()