Metadata-Version: 2.1
Name: MSMetaEnhancer
Version: 0.2.3
Summary: Repository for tool that adds more annotations (e.g. SMILES, InChI, CAS number) to MSP files (Python version).
Home-page: https://github.com/RECETOX/MSMetaEnhancer
Author: Matej Trojak
Author-email: matej.trojak@recetox.muni.cz
Maintainer: RECETOX
Maintainer-email: GalaxyToolsDevelopmentandDeployment@space.muni.cz
License: MIT
Description: ## MSMetaEnhancer
        
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/msmetaenhancer/README.html)
        [![docs](https://readthedocs.org/projects/msmetaenhancer/badge/?version=latest)](https://msmetaenhancer.readthedocs.io/en/latest/)
        [![Conda](https://img.shields.io/conda/v/bioconda/msmetaenhancer)](https://anaconda.org/bioconda/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](https://cactus.nci.nih.gov/chemical/structure_documentation), [CTS](https://cts.fiehnlab.ucdavis.edu/), [NLM](https://chem.nlm.nih.gov), [PubChem](https://pubchem.ncbi.nlm.nih.gov/), [IDSM](https://idsm.elixir-czech.cz/), and [BridgeDB](https://bridgedb.github.io/).
        The app uses asynchronous implementation of annotation process allowing for optimal fetching speed.
        
        ### Usage
        
        ```python
        import asyncio
        
        from MSMetaEnhancer import Application
        
        app = Application()
        
        # import your .msp file
        app.load_spectra('tests/test_data/sample.msp', file_format='msp')
        
        # curate given metadata (e.g. fix CAS numbers)
        app.curate_spectra()
        
        # specify requested services (these are supported)
        services = ['CTS', 'CIR', 'NLM', '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))
        
        # execute without jobs parameter to run all possible jobs
        asyncio.run(app.annotate_spectra(services))
        
        # export .msp file 
        app.save_spectra('tests/test_data/sample_out.msp', file_format='msp')
        ```
        
        ### Installation
        
        Prerequisites:
        
        - Python 3.7 or 3.8
        - Anaconda
        
        Install `MSMetaEnhancer` from Bioconda with:
        
        ```
        # install MSMetaEnhancer in a new virtual environment to avoid dependency clashes
        conda create --name MSMetaEnhancer python=3.8
        conda activate MSMetaEnhancer
        conda install --channel bioconda --channel conda-forge MSMetaEnhancer
        ```
        
        ### Developer Documentation
        
        #### Setup
        
        Create your development environment using the provided [script](conda/environment-dev.yml) 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](CHANGELOG.md) and to adhere to the [versioning](https://semver.org/spec/v2.0.0.html).
        For more information see [here](CONTRIBUTING.md).
        
        #### Testing
        
        All functionality is tested with the [pytest](https://docs.pytest.org/en/6.2.x/contents.html) framework.
        
Platform: UNKNOWN
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: test
