https://github.com/midnighter/metanetx-sdk

Parse and process information from MetaNetX for MIRIAM compatibility using the Identifiers.org registries.
https://github.com/midnighter/metanetx-sdk

bioinformatics identifiers-org metanetx miriam sdk

Last synced: 11 days ago
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Parse and process information from MetaNetX for MIRIAM compatibility using the Identifiers.org registries.

• Host: GitHub
• URL: https://github.com/midnighter/metanetx-sdk
• Owner: Midnighter
• License: apache-2.0
• Created: 2019-09-15T15:09:07.000Z (about 5 years ago)
• Default Branch: stable
• Last Pushed: 2021-09-26T13:51:09.000Z (about 3 years ago)
• Last Synced: 2024-10-03T09:46:55.379Z (about 2 months ago)
• Topics: bioinformatics, identifiers-org, metanetx, miriam, sdk
• Language: Python
• Size: 113 KB
• Stars: 5
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • Changelog: CHANGELOG.rst
  • Contributing: .github/CONTRIBUTING.rst
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.md

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README

        
============

MetaNetX SDK

============

.. image:: https://img.shields.io/pypi/v/metanetx-sdk.svg

   :target: https://pypi.org/project/metanetx-sdk/

   :alt: Current PyPI Version

.. image:: https://img.shields.io/pypi/pyversions/metanetx-sdk.svg

   :target: https://pypi.org/project/metanetx-sdk/

   :alt: Supported Python Versions

.. image:: https://img.shields.io/pypi/l/metanetx-sdk.svg

   :target: https://www.apache.org/licenses/LICENSE-2.0

   :alt: Apache Software License Version 2.0

.. image:: https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg

   :target: https://github.com/Midnighter/metanetx-sdk/blob/stable/.github/CODE_OF_CONDUCT.md

   :alt: Code of Conduct

.. image:: https://github.com/Midnighter/metanetx-sdk/workflows/CI-CD/badge.svg

   :target: https://github.com/Midnighter/metanetx-sdk/workflows/CI-CD

   :alt: GitHub Actions

.. image:: https://codecov.io/gh/Midnighter/metanetx-sdk/branch/stable/graph/badge.svg

   :target: https://codecov.io/gh/Midnighter/metanetx-sdk

   :alt: Codecov

.. image:: https://img.shields.io/badge/code%20style-black-000000.svg

   :target: https://github.com/ambv/black

   :alt: Code Style Black

.. summary-start

Parse and process information from `MetaNetX `_ for

`MIRIAM `_ compatibility using the

`Identifiers.org `_ namespaces.

Install

=======

It's as simple as:

.. code-block:: console

    pip install metanetx-sdk

Usage

=====

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

the commands' help.

.. code-block:: console

    mnx-sdk -h

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

.. code-block:: console

    mnx-sdk pull ./data

and then transforming each data table.

.. code-block:: console

    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.

Copyright

=========

* Copyright © 2019-2020, Moritz E. Beber.

* Free software distributed under the `Apache Software License 2.0 

  `_.

.. summary-end