| Name | MSMetaEnhancer JSON |
| Version |
0.3.0
JSON |
| download |
| home_page | https://github.com/RECETOX/MSMetaEnhancer |
| Summary | Repository for tool that adds more annotations (e.g. SMILES, InChI, CAS number) to MSP files (Python version). |
| upload_time | 2023-05-12 07:36:30 |
| maintainer | RECETOX |
| docs_url | None |
| author | Matej Trojak |
| requires_python | >=3.9 |
| license | MIT |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
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## MSMetaEnhancer
[](http://bioconda.github.io/recipes/msmetaenhancer/README.html)
[](https://msmetaenhancer.readthedocs.io/en/latest/)
[](https://anaconda.org/bioconda/msmetaenhancer)
[](https://doi.org/10.21105/joss.04494)
**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/), [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.
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
```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_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_spectra('tests/test_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](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.
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"description": "## MSMetaEnhancer\n\n[](http://bioconda.github.io/recipes/msmetaenhancer/README.html)\n[](https://msmetaenhancer.readthedocs.io/en/latest/)\n[](https://anaconda.org/bioconda/msmetaenhancer)\n[](https://doi.org/10.21105/joss.04494)\n\n**MSMetaEnhancer** is a tool used for `.msp` files annotation.\nIt 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/), [PubChem](https://pubchem.ncbi.nlm.nih.gov/), [IDSM](https://idsm.elixir-czech.cz/), and [BridgeDb](https://bridgedb.github.io/).\nThe app uses asynchronous implementation of annotation process allowing for optimal fetching speed.\n\nIf you use MSMetaEnhancer in your work, please cite the following publication:\n\nTroj\u00e1k 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\n### Usage\n\n```python\nimport asyncio\n\nfrom MSMetaEnhancer import Application\n\napp = Application()\n\n# import your .msp file\napp.load_spectra('tests/test_data/sample.msp', file_format='msp')\n\n# curate given metadata (e.g. fix CAS numbers)\napp.curate_metadata()\n\n# specify requested services (these are supported)\nservices = ['CTS', 'CIR', 'IDSM', 'PubChem', 'BridgeDb', 'RDKit']\n\n# specify requested jobs\njobs = [('name', 'inchi', 'IDSM'), ('inchi', 'formula', 'IDSM'), ('inchi', 'inchikey', 'IDSM'),\n ('inchi', 'iupac_name', 'IDSM'), ('inchi', 'canonical_smiles', 'IDSM')]\n\n# run asynchronous annotations of spectra data\nasyncio.run(app.annotate_spectra(services, jobs))\n\n# export .msp file \napp.save_spectra('tests/test_data/sample_out.msp', file_format='msp')\n```\n\n### Installation\n\nPrerequisites:\n\n- Python 3.9+\n- Anaconda\n\nInstall `MSMetaEnhancer` from Bioconda with:\n\n```\n# install MSMetaEnhancer in a new virtual environment to avoid dependency clashes\nconda create --name MSMetaEnhancer python=3.9\nconda activate MSMetaEnhancer\nconda install --channel bioconda --channel conda-forge MSMetaEnhancer\n```\n\n### Developer Documentation\n\n#### Setup\n\nCreate your development environment using the provided [script](conda/environment-dev.yml) via conda to install all required dependencies.\n\n#### Contributing\n\nWe appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and post a PR. \nPlease add your contributions to the [changelog](CHANGELOG.md) and to adhere to the [versioning](https://semver.org/spec/v2.0.0.html).\nFor more information see [here](CONTRIBUTING.md).\n\n#### Testing\n\nAll functionality is tested with the [pytest](https://docs.pytest.org/en/6.2.x/contents.html) framework.\n",
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