Metadata-Version: 1.1
Name: nmrml2isa
Version: 0.2.3
Summary: nmrml2isa - nmrML to ISA-Tab parsing tool
Home-page: http://github.com/althonos/nmrml2isa
Author: Martin Larralde
Author-email: martin.larralde@ens-cachan.fr
License: GPLv3
Description: nmrml2isa
        =========
        
        Parser to get meta information from nmrML file and parse relevant information to an ISA-Tab structure
        ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
        
        
        |Version| |Py versions| |Git| |Build Status| |License| |RTD doc| |DOI|
        
        
        Overview
        --------
        
        nmrml2isa is a Python3 program that can be used to generate an ISA-Tab structured
        investigation out of nmrML files, providing the backbone of a study that can then be
        edited with an ISA editing tool (see `MetaboLights pre-packaged
        ISA Creator <http://www.ebi.ac.uk/metabolights/>`__)
        
        Install
        -------
        
        See the `Installation page <http://2isa.readthedocs.io/en/latest/nmrml2isa/install.html>`__ of
        the `online documentation <http://2isa.readthedocs.io/en/latest/nmrml2isa/index.html>`__.
        
        
        Use
        ---
        
        See the `Usage page <http://2isa.readthedocs.io/en/latest/nmrml2isa/usage.html>`__ and
        the `Examples page <http://2isa.readthedocs.io/en/latest/nmrml2isa/examples.html>`__ for
        more detailed descriptions of usage and examples.
        
        CLI
        ~~~
        
        The parser comes with a simple one-liner:
        
        .. code:: bash
        
           mzml2isa -i /path/to/nmrml_files/ -o /path/to/out_folder -s name_of_study
        
        
        Module
        ~~~~~~
        
        It possible to import **nmrml2isa** as a Python module:
        
        .. code:: python
        
           from nmrml2isa import parsing
        
           in_dir = "/path/to/nmrml_files/"
           out_dir = "/path/to/out_folder/"
           study_identifier_name = "name_of_study"
        
           parsing.full_parse(in_dir, out_dir, study_identifier_name)
        
        
        Meta extraction
        ~~~~~~~~~~~~~~~~
        
        If you just want to extract the meta information without writing them
        in ISA-Tab files, it is possible to do so either by running the ``nmrml2isa.nmrml``
        module as main:
        
        .. code:: bash
        
           python -m nmrml2isa.nmrml /path/to/your/file.nmrML
           # this will produce a JSON dict of all extracted metadata
        
        
        Or within a python program with the **nmrml** submodule:
        
        .. code:: python
        
           from nmrml2isa import nmrml
        
           nmrml_path = "/path/to/file.nmrML"
           nmrml_meta = nmrml.nmrMLmeta(nmrml_path)
        
           # python dictionnary
           print(nmrml_meta.meta)
        
           # json dictionnary
           print(nmrml_meta.meta_json)
        
        
        
        
        .. |Build Status| image:: https://img.shields.io/travis/althonos/nmrml2isa.svg?style=flat&maxAge=2592000
           :target: https://travis-ci.org/althonos/nmrml2isa
        
        .. |Py versions| image:: https://img.shields.io/pypi/pyversions/nmrml2isa.svg?style=flat&maxAge=2592000
           :target: https://pypi.python.org/pypi/nmrml2isa/
        
        .. |Version| image:: https://img.shields.io/pypi/v/nmrml2isa.svg?style=flat&maxAge=2592000
           :target: https://pypi.python.org/pypi/nmrml2isa/
        
        .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=2592000
           :target: https://github.com/althonos/nmrml2isa
        
        .. |License| image:: https://img.shields.io/pypi/l/nmrml2isa.svg?style=flat&maxAge=2592000
           :target: https://www.gnu.org/licenses/gpl-3.0.html
        
        .. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=2592000
           :target: http://2isa.readthedocs.io/en/latest/nmrml2isa/index.html
        
        .. |DOI| image:: https://zenodo.org/badge/23304/althonos/nmrml2isa.svg
           :target: https://zenodo.org/badge/latestdoi/23304/althonos/nmrml2isa
        
Keywords: Metabolomics,NMR,Nuclear Magnetic Resonance,ISA Tab,nmrML,metabolites,parsing
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Text Processing :: Markup :: XML
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Utilities
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
