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Parse and process information from MetaNetX for MIRIAM compatibility using the Identifiers.org registries.

License: Apache License 2.0

Makefile 3.95% Python 96.05%
metanetx sdk miriam identifiers-org bioinformatics

metanetx-sdk's Introduction

MetaNetX SDK

Current PyPI Version Supported Python Versions Apache Software License Version 2.0 Code of Conduct GitHub Actions Codecov Code Style Black

Parse and process information from MetaNetX for MIRIAM compatibility using the Identifiers.org namespaces.

Install

It's as simple as:

pip install metanetx-sdk

Usage

The authoritative source on how to use the various commands is always accessible via the commands' help.

mnx-sdk -h

Normally you would start by loading the files from the MetaNetX FTP server

mnx-sdk pull ./data

and then transforming each data table.

mnx-sdk etl chem-prop ./data/chem_prop.tsv.gz ./data/transformed_chem_prop.tsv.gz

You can also directly use the functions from the metanetx_sdk.api module.

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