mwtab

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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 @ Pages_


Installation

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 Pages_
          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
.. _Pages: https://moseleybioinformaticslab.github.io/mwtab/
.. _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