Metadata-Version: 1.1
Name: mwtab
Version: 0.1.7
Summary: Parser for mwtab files from the Metabolomics Workbench
Home-page: https://github.com/MoseleyBioinformaticsLab/mwtab
Author: Andrey Smelter
Author-email: andrey.smelter@gmail.com
License: BSD
Description: 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://api.travis-ci.org/MoseleyBioinformaticsLab/mwtab.svg?branch=master
           :target: https://travis-ci.org/MoseleyBioinformaticsLab/mwtab
           :alt: Travis CI status
        
        .. image:: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab/branch/master/graphs/badge.svg?branch=master
           :target: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab
           :alt: Code coverage information
        
        
        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 JSONized 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.
        
        
        Links
        ~~~~~
        
           * mwtab @ GitHub_
           * mwtab @ PyPI_
           * Documentation @ ReadTheDocs_
        
        
        Installation
        ~~~~~~~~~~~~
        
        The `mwtab` package runs under Python 2.7 and Python 3.4+. 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.
        
        
        File Formatting Issues
        ~~~~~~~~~~~~~~~~~~~~~~
        
        Currently there are 5 files that are failing to parse due to formatting issues
        within them:
        
           * ST000258_AN000410.txt
        
              - extra tab character on line 360 ('MS_ALL_DATA:UNITS   \t\t')
        
           * ST000365_AN000598.txt
        
              - ST:EMAIL line is broken on line 53, 54 ('ST:EMAIL            \n@unc.edu')
              - extra tab on line 155 ('NMR_BINNED_DATA:UNITS\tppm\t')
        
           * ST000445_AN000696.txt
        
              - extra tab character on line 135 ('CH:CHROMATOGRAPHY_SUMMARY     \t\tThe gradient composition was changed linearly from 50% to 100% solvent B')
        
           * ST000901_AN001467.txt
        
              - extra tab character on lines 61-78  ('SP:SAMPLEPREP_SUMMARY            \tPreparation of SPE on vacuum manifold: 1.\tClean 60 mg Oasis HLB (Waters) spe ...')
        
           * ST000902_AN001468.txt
        
              - Header line is broken into two lines on lines 1-2 ('#METABOLOMICS WORKBENCH hover_20170726_173354 DATATRACK_ID:1171\n STUDY_ID:ST000902 ANALYSIS_ID:AN001468')
        
        
        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/
        
Keywords: mwtab metabolomics workbench
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
