mzrt2h5 0.1.0

A package to convert mzML files to HDF5 for deep learning.

mzrt2h5

A Python package to convert mzML files to HDF5 format for deep learning applications.

Installation

pip install -r requirements.txt
pip install .

Usage

from mzrt2h5.processing import save_dataset_as_sparse_h5
from mzrt2h5.dataset import DynamicSparseH5Dataset

# Process mzML files and save to HDF5
save_dataset_as_sparse_h5(
    folder="path/to/your/mzML_files",
    save_path="output.h5",
    rt_precision=0.1,
    mz_precision=0.01,
    metadata_csv_path="path/to/your/metadata.csv",
)

# Create a PyTorch dataset
dataset = DynamicSparseH5Dataset(
    h5_path="output.h5",
    target_rt_precision=0.5,
    target_mz_precision=0.05,
)