msp2db

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)