mwtab

The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.

https://github.com/moseleybioinformaticslab/mwtab

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Repository

The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.

README.rst

mwtab
=====

.. image:: https://img.shields.io/pypi/l/mwtab.svg
   :target: https://choosealicense.com/licenses/bsd-3-clause-clear/
   :alt: License information

.. image:: https://img.shields.io/pypi/v/mwtab.svg
   :target: https://pypi.org/project/mwtab
   :alt: Current library version

.. image:: https://img.shields.io/pypi/pyversions/mwtab.svg
   :target: https://pypi.org/project/mwtab
   :alt: Supported Python versions

.. image:: https://readthedocs.org/projects/nmrstarlib/badge/?version=latest
   :target: http://mwtab.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation status

.. image:: https://github.com/MoseleyBioinformaticsLab/mwtab/actions/workflows/build.yml/badge.svg
   :target: https://github.com/MoseleyBioinformaticsLab/mwtab/actions/workflows/build.yml
   :alt: Build status

.. image:: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab/branch/master/graph/badge.svg?token=jhjMsP1qma
   :target: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab
   :alt: CodeCov

.. image:: https://img.shields.io/badge/DOI-10.3390%2Fmetabo11030163-blue.svg
   :target: https://doi.org/10.3390/metabo11030163
   :alt: Citation link

.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/mwtab.svg?style=social&label=Star
   :target: https://github.com/MoseleyBioinformaticsLab/mwtab
   :alt: GitHub project

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.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/mwtab/master/docs/_static/images/mwtab_logo.png
   :width: 50%
   :align: center
   :target: http://mwtab.readthedocs.io/


The ``mwtab`` package is a Python library that facilitates reading and writing
files in ``mwTab`` format used by the `Metabolomics Workbench`_ for archival of
Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.

The ``mwtab`` package provides facilities to convert ``mwTab`` formatted files into
their equivalent ``JSON`` ized representation and vice versa.  ``JSON`` stands for JavaScript
Object Notation, an open-standard format that uses human-readable text to transmit
data objects consisting of attribute-value pairs.

The ``mwtab`` package can be used in several ways:

   * As a library for accessing and manipulating data stored in ``mwTab`` format files.
   * As a command-line tool to convert between ``mwTab`` format and its equivalent
     ``JSON`` representation.


Citation
~~~~~~~~

When using ``mwtab`` package in published work, please cite the following papers:

   * Powell, Christian D., and Hunter NB Moseley. "The mwtab Python Library for RESTful
     Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics
     Workbench Data Repository." *Metabolites* 11.3 (2021): 163. doi:
     `10.3390/metabo11030163`_.

   * Smelter, Andrey and Hunter NB Moseley. "A Python library for FAIRer access and
     deposition to the Metabolomics Workbench Data Repository."
     *Metabolomics* 2018, 14(5): 64. doi: `10.1007/s11306-018-1356-6`_.


Links
~~~~~

   * mwtab @ GitHub_
   * mwtab @ PyPI_
   * Documentation @ ReadTheDocs_


Installation
~~~~~~~~~~~~

The ``mwtab`` package runs under Python 3.5+. Use pip_ to install.
Starting with Python 3.4, pip_ is included by default.


Install on Linux, Mac OS X
--------------------------

.. code:: bash

   python3 -m pip install mwtab


Install on Windows
------------------

.. code:: bash

   py -3 -m pip install mwtab


Upgrade on Linux, Mac OS X
--------------------------

.. code:: bash

   python3 -m pip install mwtab --upgrade


Upgrade on Windows
------------------

.. code:: bash

   py -3 -m pip install mwtab --upgrade


Quickstart
~~~~~~~~~~

.. code:: python

   >>> import mwtab
   >>>
   >>> # Here we use ANALYSIS_ID of file to fetch data from URL
   >>> for mwfile in mwtab.read_files("1", "2"):
   ...      print("STUDY_ID:", mwfile.study_id)
   ...      print("ANALYSIS_ID:", mwfile.analysis_id)
   ...      print("SOURCE:", mwfile.source)
   ...      print("Blocks:", list(mwfile.keys()))
   >>>


.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/mwtab/master/docs/_static/images/mwtab_demo.gif
   :align: center


.. note:: Read the User Guide and the ``mwtab`` Tutorial on ReadTheDocs_
          to learn more and to see code examples on using the ``mwtab`` as a
          library and as a command-line tool.


License
~~~~~~~

This package is distributed under the BSD_ `license`.


.. _Metabolomics Workbench: http://www.metabolomicsworkbench.org
.. _GitHub: https://github.com/MoseleyBioinformaticsLab/mwtab
.. _ReadTheDocs: http://mwtab.readthedocs.io
.. _PyPI: https://pypi.org/project/mwtab
.. _pip: https://pip.pypa.io
.. _BSD: https://choosealicense.com/licenses/bsd-3-clause-clear/
.. _10.3390/metabo11030163: https://doi.org/10.3390/metabo11030163
.. _10.1007/s11306-018-1356-6: http://dx.doi.org/10.1007/s11306-018-1356-6

Owner

Citation (CITATION.cff)

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Powell"
  given-names: "Christian"
  orcid: "https://orcid.org/0000-0002-4242-080X"
- family-names: "Smelter"
  given-names: "Andrey"
  orcid: "https://orcid.org/0000-0003-3056-9225"
- family-names: "Moseley"
  given-names: "Hunter"
  orcid: "https://orcid.org/0000-0003-3995-5368"
title: "mwtab"
version: 1.2.5
date-released: 2017-03-18
url: "https://github.com/MoseleyBioinformaticsLab/mwtab"
preferred-citation:
  type: article
  authors:
  - family-names: "Powell"
    given-names: "Christian"
    orcid: "https://orcid.org/0000-0002-4242-080X"
  - family-names: "Moseley"
    given-names: "Hunter"
    orcid: "https://orcid.org/0000-0003-3995-5368"
  doi: "10.3390/metabo11030163"
  journal: "Metabolites"
  month: 3
  title: "The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository"
  issue: 11
  volume: 3
  year: 2021

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