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Python package for converting msp to database

Project description

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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 or as MoNA records.

The resulting SQLite database can be used for spectral matching with msPurity Bioconductor R package, see vigenette.

Installation

$ pip install .

Command line

$ msp2db -msp_pth [msp file or directory of msp files] -name [name of database] -source [name of source of msp e.g. massbank] -o [out dir]
$ msp2db --help

API

db_pth = '/home/tomnl/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)

Project details


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