mwtab
=====
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.. image:: https://img.shields.io/badge/DOI-10.3390%2Fmetabo11030163-blue.svg
:target: https://doi.org/10.3390/metabo11030163
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|
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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 @ 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
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"description": "mwtab\n=====\n\n.. image:: https://img.shields.io/pypi/l/mwtab.svg\n :target: https://choosealicense.com/licenses/bsd-3-clause-clear/\n :alt: License information\n\n.. image:: https://img.shields.io/pypi/v/mwtab.svg\n :target: https://pypi.org/project/mwtab\n :alt: Current library version\n\n.. image:: https://img.shields.io/pypi/pyversions/mwtab.svg\n :target: https://pypi.org/project/mwtab\n :alt: Supported Python versions\n\n.. image:: https://readthedocs.org/projects/nmrstarlib/badge/?version=latest\n :target: http://mwtab.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation status\n\n.. image:: https://github.com/MoseleyBioinformaticsLab/mwtab/actions/workflows/build.yml/badge.svg\n :target: https://github.com/MoseleyBioinformaticsLab/mwtab/actions/workflows/build.yml\n :alt: Build status\n\n.. image:: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab/branch/master/graph/badge.svg?token=jhjMsP1qma\n :target: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab\n :alt: CodeCov\n\n.. image:: https://img.shields.io/badge/DOI-10.3390%2Fmetabo11030163-blue.svg\n :target: https://doi.org/10.3390/metabo11030163\n :alt: Citation link\n\n.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/mwtab.svg?style=social&label=Star\n :target: https://github.com/MoseleyBioinformaticsLab/mwtab\n :alt: GitHub project\n\n|\n\n.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/mwtab/master/docs/_static/images/mwtab_logo.png\n :width: 50%\n :align: center\n :target: http://mwtab.readthedocs.io/\n\n\nThe ``mwtab`` package is a Python library that facilitates reading and writing\nfiles in ``mwTab`` format used by the `Metabolomics Workbench`_ for archival of\nMass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.\n\nThe ``mwtab`` package provides facilities to convert ``mwTab`` formatted files into\ntheir equivalent ``JSON`` ized representation and vice versa. ``JSON`` stands for JavaScript\nObject Notation, an open-standard format that uses human-readable text to transmit\ndata objects consisting of attribute-value pairs.\n\nThe ``mwtab`` package can be used in several ways:\n\n * As a library for accessing and manipulating data stored in ``mwTab`` format files.\n * As a command-line tool to convert between ``mwTab`` format and its equivalent\n ``JSON`` representation.\n\n\nCitation\n~~~~~~~~\n\nWhen using ``mwtab`` package in published work, please cite the following papers:\n\n * Powell, Christian D., and Hunter NB Moseley. \"The mwtab Python Library for RESTful\n Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics\n Workbench Data Repository.\" *Metabolites* 11.3 (2021): 163. doi:\n `10.3390/metabo11030163`_.\n\n * Smelter, Andrey and Hunter NB Moseley. \"A Python library for FAIRer access and\n deposition to the Metabolomics Workbench Data Repository.\"\n *Metabolomics* 2018, 14(5): 64. doi: `10.1007/s11306-018-1356-6`_.\n\n\nLinks\n~~~~~\n\n * mwtab @ GitHub_\n * mwtab @ PyPI_\n * Documentation @ ReadTheDocs_\n\n\nInstallation\n~~~~~~~~~~~~\n\nThe ``mwtab`` package runs under Python 3.5+. Use pip_ to install.\nStarting with Python 3.4, pip_ is included by default.\n\n\nInstall on Linux, Mac OS X\n--------------------------\n\n.. code:: bash\n\n python3 -m pip install mwtab\n\n\nInstall on Windows\n------------------\n\n.. code:: bash\n\n py -3 -m pip install mwtab\n\n\nUpgrade on Linux, Mac OS X\n--------------------------\n\n.. code:: bash\n\n python3 -m pip install mwtab --upgrade\n\n\nUpgrade on Windows\n------------------\n\n.. code:: bash\n\n py -3 -m pip install mwtab --upgrade\n\n\nQuickstart\n~~~~~~~~~~\n\n.. code:: python\n\n >>> import mwtab\n >>>\n >>> # Here we use ANALYSIS_ID of file to fetch data from URL\n >>> for mwfile in mwtab.read_files(\"1\", \"2\"):\n ... print(\"STUDY_ID:\", mwfile.study_id)\n ... print(\"ANALYSIS_ID:\", mwfile.analysis_id)\n ... print(\"SOURCE:\", mwfile.source)\n ... print(\"Blocks:\", list(mwfile.keys()))\n >>>\n\n\n.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/mwtab/master/docs/_static/images/mwtab_demo.gif\n :align: center\n\n\n.. note:: Read the User Guide and the ``mwtab`` Tutorial on ReadTheDocs_\n to learn more and to see code examples on using the ``mwtab`` as a\n library and as a command-line tool.\n\n\nLicense\n~~~~~~~\n\nThis package is distributed under the BSD_ `license`.\n\n\n.. _Metabolomics Workbench: http://www.metabolomicsworkbench.org\n.. _GitHub: https://github.com/MoseleyBioinformaticsLab/mwtab\n.. _ReadTheDocs: http://mwtab.readthedocs.io\n.. _PyPI: https://pypi.org/project/mwtab\n.. _pip: https://pip.pypa.io\n.. _BSD: https://choosealicense.com/licenses/bsd-3-clause-clear/\n.. _10.3390/metabo11030163: https://doi.org/10.3390/metabo11030163\n.. _10.1007/s11306-018-1356-6: http://dx.doi.org/10.1007/s11306-018-1356-6\n\n\n",
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