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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] --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

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)

Project details


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