mspCMSI

Usage

If you haven't installed the package (see installation section below) then the commands must be run from the mspCMSI/mspCSMI directory containing the code

Create "Database"

First, create a "database" (metadata .tsv file + a binary pickle file containing spectra) from an msp file by running

python mspCSMI.py makeDB <mspFile.msp> <metaDataFile.tsv> <spectrumFile.pkl>

This will create a .tsv file in the location specified by <metaDataFile.tsv>. For now, this file can be used for querying the contents of the MSP file

Get Spectrum

Once you've found an interesting spectrum's index, get the spectrum by running

python mspCSMI.py getSpectrum <spectrumIndex> <spectrumFile.pkl> [<outFile>]

Optionally including a tab-separated to write to (e.g. (otherwise the spectrum will just print to stdout)

Plot Spectra

A spectrum plot can be created by running

python mspCSMI.py plotSpectrum <spectrumIndex> <spectrumFile.msp> <outFile>

Here <outFile> is required

(Optional) Installation

Should be able to run the following command from the top directory

pip install .

to install the mspCMSI package. If installed succesfully, you should be able to run the commands above from anywhere and can write "mspCSMI" instead of "python mspCSMI.py" for example:

mspCSMI plotSpectrum <spectrumIndex> <spectrumFile.msp> <outFile>