Metadata-Version: 1.1
Name: mzml2isa
Version: 0.4.19
Summary: mzml2isa - mzML to ISA-tab parsing tool
Home-page: http://www.biosciences.bham.ac.uk/labs/viant/
Author: Thomas Lawson, Martin Larralde
Author-email: tnl495@bham.ac.uk
License: GPLv3
Description: mzml2isa
        ========
        
        Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure
        
        |Version| |Py versions| |Git| |Build Status| |License| |RTD doc|
        
        Overview
        --------
        
        mzml2isa is a Python3 program that can be used to generate an ISA-Tab
        structure out of mzML files, providing the backbone of a study which can
        then be edited with an ISA editing tool (see `MetaboLights pre-packaged
        ISA Creator <http://www.ebi.ac.uk/metabolights/>`__)
        
        Currently the program does the following:
          * Extract meta information from mzML files and store as either python dictionary or JSON format
          * Create an ISA-Tab file structure with relevant meta information
          * Add additional metadata that cannot be parsed from mzML files to the ISA-Tab files through a JSON formatted dictionnary.
        
        Install
        -------
        
        See the `Installation page <http://2isa.readthedocs.io/en/latest/mzml2isa/install.html>`__ of
        the `online documentation <http://2isa.readthedocs.io/en/latest/mzml2isa/index.html>`__.
        
        Usage
        -----
        
        CLI
        '''
        
        .. code:: bash
        
            mzml2isa -i /path/to/mzml_files/ -o /path/to/out_folder/ -s name_of_study
        
        Python Module
        '''''''''''''
        
        See the `Usage page <http://2isa.readthedocs.io/en/latest/mzml2isa/usage.html>`__ and
        the `Examples page <http://2isa.readthedocs.io/en/latest/mzml2isa/examples.html>`__ for more
        information.
        
        
        
        Metabolights
        ------------
        
        To download some real data from
        `MetaboLights <http://www.ebi.ac.uk/metabolights/>`__ studies to test
        the converter with, run
        
        .. code:: bash
        
            python scripts/metabolights-dl.py <size>
        
        from inside the repository, where *size* is the maximum size in GiB you
        can allocate to download files. The script will download the files to
        the ``example_files/metabolight``\ s folder and then run mzml2isa on
        those files..
        
        If you use a \*NIX machine with **curlftpfs** and **bash** available,
        you can also run
        
        .. code:: bash
        
            scripts/metabolights.sh
        
        to mount the database to the example directory and start converting mzML
        studies.
        
        Workflow
        --------
        
        .. figure:: https://raw.githubusercontent.com/Tomnl/mzml2isa/master/isa_config/mzml2isa.png
           :alt: workflow
        
        Ref
        ---
        
        A modified version of the ontology extraction from this blog [1]_ was
        used, and a slightly modified class from pymzml [2]_
        
        .. [1] http://blog.nextgenetics.net/?e=6
        .. [2] http://pymzml.github.io/
        
        
        .. |Build Status| image:: https://img.shields.io/travis/althonos/mzml2isa.svg?style=flat&maxAge=2592000
           :target: https://travis-ci.org/althonos/mzml2isa
        
        .. |Py versions| image:: https://img.shields.io/pypi/pyversions/mzml2isa.svg?style=flat&maxAge=2592000
           :target: https://pypi.python.org/pypi/mzml2isa/
        
        .. |Version| image:: https://img.shields.io/pypi/v/mzml2isa.svg?style=flat&maxAge=2592000
           :target: https://pypi.python.org/pypi/mzml2isa/
        
        .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=2592000
           :target: https://github.com/althonos/mzml2isa
        
        .. |License| image:: https://img.shields.io/pypi/l/mzml2isa.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/mzml2isa/index.html
        
Keywords: Metabolomics,Mass spectrometry,metabolites,ISA Tab,mzML,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
