Hdf5 validator package
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
- 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.
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
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.
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/
h5_validate multi_read_fast5.yaml /data/multi_read.fast5 -v
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