#!/usr/bin/env python
import os
import sys
import argparse
import gzip
from time import gmtime, strftime
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

class Tree(object):
    """Tree node used in constructing taxonomy tree."""
    def __init__(self, taxid, level_num, level_id, children=None, parent=None):
        self.taxid = taxid
        self.level_num = level_num
        self.level_id = level_id
        self.children = []
        self.parent = parent
        if children is not None:
            for child in children:
                self.add_child(child)
                
    def add_child(self, node):
        assert isinstance(node, Tree)
        self.children.append(node)

def process_kraken_output(kraken_line):
    l_vals = kraken_line.split('\t')
    if len(l_vals) < 5:
        return [-1, '']
    tax_id = l_vals[2].split("taxid ")[-1] if "taxid" in l_vals[2] else l_vals[2]
    tax_id = 81077 if tax_id == 'A' else int(tax_id)
    return [tax_id, l_vals[1]]

def process_kraken_report(report_line):
    l_vals = report_line.strip().split('\t')
    if len(l_vals) < 5:
        return []
    try:
        int(l_vals[1])
    except ValueError:
        return []
    taxid = int(l_vals[-3])
    level_type = l_vals[-2]
    map_kuniq = {'species': 'S', 'genus': 'G', 'family': 'F', 'order': 'O', 'class': 'C', 'phylum': 'P', 'superkingdom': 'D', 'kingdom': 'K'}
    level_type = map_kuniq.get(level_type, '-')
    level_num = int(sum(1 for char in l_vals[-1] if char == ' ') / 2)
    return [taxid, level_num, level_type]

def extract_reads_i(args):
    # Your program logic using args (parsed arguments passed as function arguments)
    # Initialize taxonomies, open files, and execute the core read extraction logic
    # -- Here you would keep the main logic of the program without direct argument parsing.
    pass

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('-k', dest='kraken_file', required=True, help='Kraken output file to parse')
    parser.add_argument('-s','-s1', '-1', '-U', dest='seq_file1', required=True, help='FASTA/FASTQ File containing the raw sequence letters.')
    parser.add_argument('-s2', '-2', dest='seq_file2', default="", help='2nd FASTA/FASTQ File containing the raw sequence letters (paired).')
    parser.add_argument('-t', "--taxid", dest='taxid', required=True, nargs='+', help='Taxonomy ID[s] of reads to extract (space-delimited)')
    parser.add_argument('-o', "--output", dest='output_file', required=True, help='Output FASTA/Q file containing the reads and sample IDs')
    parser.add_argument('-o2', "--output2", dest='output_file2', required=False, default='', help='Output FASTA/Q file containing the second pair of reads [required for paired input]')
    parser.add_argument('--append', dest='append', action='store_true', help='Append the sequences to the end of the output FASTA file specified.')
    parser.add_argument('--noappend', dest='append', action='store_false', help='Create a new FASTA file (rewrite if existing) [default].')
    parser.add_argument('--max', dest='max_reads', required=False, default=100000000, type=int, help='Maximum number of reads to save [default: 100,000,000]')
    parser.add_argument('-r', '--report', dest='report_file', required=False, default="", help='Kraken report file. [required only if --include-parents/children is specified]')
    parser.add_argument('--include-parents', dest="parents", required=False, action='store_true', default=False, help='Include reads classified at parent levels of the specified taxids')
    parser.add_argument('--include-children', dest='children', required=False, action='store_true', default=False, help='Include reads classified more specifically than the specified taxids')
    parser.add_argument('--exclude', dest='exclude', required=False, action='store_true', default=False, help='Finds all reads NOT matching specified taxids')
    parser.add_argument('--fastq-output', dest='fastq_out', required=False, action='store_true', default=False, help='Print output FASTQ reads [default: output is FASTA]')
    parser.set_defaults(append=False)

    args = parser.parse_args()
    extract_reads_i(args)

if __name__ == "__main__":
    main()
