H5 Validator - Validation tool for testing Fast5 files against the schema

ont_h5_validator is a simple tool for validating the structure of fast5 files against the file schema maintained by Oxford Nanopore Technologies

• Source code: https://github.com/nanoporetech/ont_h5_validator

It provides:

• Command line validation tools for validating fast5 files
• Json format data schemas specifying the fast5 standard

NB The h5_validator is intended as a tool to validate the output of the latest MinKNOW-core. The schemas are currently intended to be restrictive and therefore additional fields (for example those added by albacore or guppy) will not be expected in the schema and flagged as invalid.

Getting Started

The ont_h5_validator is available on PyPI and can be installed via pip:

pip install ont-h5-validator

Alternatively it is available on github where it can be built from source:

git clone https://github.com/nanoporetech/ont_h5_validator
cd ont_h5_validator
python setup.py install

Dependencies

ont_h5_validator is a pure python project and should run on most python versions and operating systems.

It requires:

• h5py
• NumPy
• PyYAML: 3.1.1 or higher

Interface - Console Scripts

The ont_h5_validator provides a console script for validating fast5 files against a JSON schema. This script is added during installation of this project and can be called from the command line or from within python.

h5_validate

This script expects:

h5_validate
    schema <(path) json schema file (see note-1)>
    filename <(path) fast5 file>
    [optional] -v, --verbose <(bool) show additional verbose output; default=False>
    [optional] --debug <(bool) include additional debug logging; default=False>

note-1: if the schema file is not found on the path specified the script will additionally look in the default directory h5_validator/schemas/

example usage:

h5_validate multi_read_fast5.yaml /data/multi_read.fast5 -v