msmetaenhancer 0.5.0

Repository for tool that adds more annotations (e.g. SMILES, InChI, CAS number) to MSP files (Python version).

MSMetaEnhancer

MSMetaEnhancer is a tool used for .msp files annotation. It adds metadata like SMILES, InChI, and CAS number fetched from the following services: CIR, CTS, PubChem, IDSM, and BridgeDb. The app uses asynchronous implementation of annotation process allowing for optimal fetching speed.

If you use MSMetaEnhancer in your work, please cite the following publication:

Troják et al., (2022). MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software, 7(79), 4494, https://doi.org/10.21105/joss.04494

Usage

import asyncio

from MSMetaEnhancer import Application
from MSMetaEnhancer.libs.converters.web import CTS, CIR, IDSM, PubChem, BridgeDb
from MSMetaEnhancer.libs.converters.compute import RDKit
from MSMetaEnhancer.libs.utils.ConverterBuilder import ConverterBuilder

ConverterBuilder.register([CTS, CIR, IDSM, PubChem, BridgeDb, RDKit])

app = Application()

# import your .msp file
app.load_data('sample.msp', file_format='msp')

# curate given metadata (e.g. fix CAS numbers)
app.curate_metadata()

# specify requested services (these are supported)
services = ['CTS', 'CIR', 'IDSM', 'PubChem', 'BridgeDb', 'RDKit']

# specify requested jobs
jobs = [('name', 'inchi', 'IDSM'), ('inchi', 'formula', 'IDSM'), ('inchi', 'inchikey', 'IDSM'),
        ('inchi', 'iupac_name', 'IDSM'), ('inchi', 'canonical_smiles', 'IDSM')]

# run asynchronous annotations of spectra data
asyncio.run(app.annotate_spectra(services, jobs))

# export .msp file
app.save_data('sample_out.msp', file_format='msp')

Installation

Prerequisites:

• Python 3.9+
• Anaconda

Install MSMetaEnhancer from Bioconda with:

# install MSMetaEnhancer in a new virtual environment to avoid dependency clashes
conda create --name MSMetaEnhancer python=3.9
conda activate MSMetaEnhancer
conda install --channel bioconda --channel conda-forge MSMetaEnhancer

Developer Documentation

Setup

Create your development environment using the provided script via conda to install all required dependencies.

Contributing

We appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and post a PR. Please add your contributions to the changelog and to adhere to the versioning. For more information see here.

Testing

All functionality is tested with the pytest framework.