<filename>meth5/main_create_m5.py
from typing import List
import argparse
import tqdm
from pathlib import Path
from meth5.meth5 import MetH5File


def main(
    chunk_size: int, input_paths: List[Path], output_file: Path, compression: str, allowed_chromosomes: List[str], quiet: bool
):
    if compression == "None":
        compression = None
    
    if allowed_chromosomes is not None and len(allowed_chromosomes) == 0:
        allowed_chromosomes = None

    input_files = []
    for input_path in input_paths:
        if not input_path.exists():
            raise ValueError(f"Cannot find path {input_path}")
        if input_path.is_file():
            input_files.append(input_path)
        elif input_path.is_dir():
            subfiles = list(input_path.iterdir())
            if len(subfiles) == 0:
                raise ValueError(f"Provided input path refers to a directory which is empty: {input_path}")
            input_files += [f for f in subfiles if f.is_file()]
    
    with MetH5File(output_file, chunk_size=chunk_size, mode="w", compression=compression) as m5_out:
        for input_file in tqdm.tqdm(input_files) if not quiet else input_files:
            m5_out.parse_and_add_nanopolish_file(
                input_file, postpone_sorting_until_close=True, include_chromosomes=allowed_chromosomes
            )
        m5_out.create_chunk_index()

<filename>meth5/main_create_m5.py
from typing import List
import argparse
import tqdm
from pathlib import Path
from meth5.meth5 import MetH5File


def main(
    chunk_size: int, input_paths: List[Path], output_file: Path, compression: str, allowed_chromosomes: List[str], quiet: bool
):
    if compression == "None":
        compression = None
    
    if allowed_chromosomes is not None and len(allowed_chromosomes) == 0:
        allowed_chromosomes = None

    input_files = []
    for input_path in input_paths:
        if not input_path.exists():
            raise ValueError(f"Cannot find path {input_path}")
        if input_path.is_file():
            input_files.append(input_path)
        elif input_path.is_dir():
            subfiles = list(input_path.iterdir())
            if len(subfiles) == 0:
                raise ValueError(f"Provided input path refers to a directory which is empty: {input_path}")
            input_files += [f for f in subfiles if f.is_file()]
    
    with MetH5File(output_file, chunk_size=chunk_size, mode="w", compression=compression) as m5_out:
        for input_file in tqdm.tqdm(input_files) if not quiet else input_files:
            m5_out.parse_and_add_nanopolish_file(
                input_file, postpone_sorting_until_close=True, include_chromosomes=allowed_chromosomes
            )
        m5_out.create_chunk_index()
