Metadata-Version: 1.1
Name: msp2db
Version: 0.0.7
Summary: Python package for converting msp to database
Home-page: https://github.com/computational-metabolomics/msp2db
Author: Thomas N. Lawson
Author-email: t.n.lawson@bham.ac.uk
License: GPLv3
Description: msp2db
        ======
        
        |Version| |Py versions| |Git| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov|
        
        Python package to create an SQLite database from a collection of MSP mass spectromertry spectra files. Currently works with MSP files formated as  `MassBank records <https://github.com/MassBank/MassBank-data>`__
        or as  `MoNA records <http://mona.fiehnlab.ucdavis.edu/downloads>`__.
        
        The resulting SQLite database can be used for spectral matching with    `msPurity Bioconductor R package <https://bioconductor.org/packages/release/bioc/html/msPurity.html>`__, see `vigenette. <https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-matching-vignette.html>`__
        
        
        
        Installation
        ------------
        ::
        
            $ pip install .
        
        Command line
        ------------
        ::
        
            $ msp2db --msp_pth [msp file or directory of msp files] --source [name of source of msp e.g. massbank] --out_pth [out dir]
            $ msp2db --help
        
            usage: PROG [-h] -m MSP_PTH -s SOURCE [-o OUT_PTH] [-t TYPE] [-d] [-l MSLEVEL]
                    [-c CHUNK] [-x SCHEMA]
        
            Convert msp to SQLite or MySQL database
        
            optional arguments:
                -h, --help            show this help message and exit
                -m MSP_PTH, --msp_pth MSP_PTH
                                        path to the MSP file (or directory of msp files)
                -s SOURCE, --source SOURCE
                                        Name of data source (e.g. MassBank, LipidBlast)
                -o OUT_PTH, --out_pth OUT_PTH
                                        file path for SQLite database
                -t TYPE, --db_type TYPE
                                        database type [mysql, sqlite]
                -d, --delete_tables   delete tables
                -l MSLEVEL, --mslevel MSLEVEL
                                        ms level of fragmentation if not detailed in msp file
                -c CHUNK, --chunk CHUNK
                                        Chunks of spectra to parse data (useful to control
                                        memory usage)
                -x SCHEMA, --schema SCHEMA
                                        Type of schema used (by default is "mona" msp style
                                        but can use "massbank" style)
        
            --------------
        
        API
        ------------
        .. code-block:: python
        
            db_pth = 'spectral_library_07112018v1.db'
            create_db(file_pth=db_pth, db_type='sqlite', db_name='spectra')
            libdata = LibraryData(msp_pth='MoNA-export-FAHFA.msp',
                              db_pth=db_pth,
                              db_type='sqlite',
                              d_form=None,
                              schema='mona',
                              source='fahfa',
                              mslevel=None,
                              chunk=200)
        
        
        
        Developers & Contributors
        -------------------------
        Tom Lawson: t.n.lawson@bham.ac.uk
        
        License
        -------
        Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/msp2db/blob/master/LICENSE>`_)
        
        
        .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/msp2db.svg?style=flat&maxAge=3600&label=Travis-CI
           :target: https://travis-ci.org/computational-metabolomics/msp2db
        
        .. |Py versions| image:: https://img.shields.io/pypi/pyversions/msp2db.svg?style=flat&maxAge=3600
           :target: https://pypi.python.org/pypi/msp2db/
          
        .. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/Tomnl/msp2db.svg?style=flat&maxAge=3600&label=AppVeyor
           :target: https://ci.appveyor.com/project/Tomnl/msp2db
        
        .. |Version| image:: https://img.shields.io/pypi/v/msp2db.svg?style=flat&maxAge=3600
           :target: https://pypi.python.org/pypi/msp2db/
        
        .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
           :target: https://github.com/ISA-tools/msp2db
        
        
        .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
           :target: https://www.gnu.org/licenses/gpl-3.0.html
        
        .. |RTD doc| image:: https://img.shields.io/readthedocs/msp2db.svg?style=flat&maxAge=3600
           :target: https://msp2db.readthedocs.io/en/latest/
           
        .. |codecov| image:: https://codecov.io/gh/computational-metabolomics/msp2db/branch/master/graph/badge.svg
          :target: https://codecov.io/gh/computational-metabolomics/msp2db
        
        
        
        
Keywords: Metabolomics,Lipidomics,Mass spectrometry,Data Processing,Fragmentation
Platform: Windows, UNIX
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
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
