Metadata-Version: 2.4
Name: omnipath-utils
Version: 0.1.0
Summary: ID translation, taxonomy, orthology and reference lists for molecular biology
Project-URL: Documentation, https://saezlab.github.io/omnipath-utils
Project-URL: Homepage, https://github.com/saezlab/omnipath-utils
Project-URL: Issues, https://github.com/saezlab/omnipath-utils/issues
Project-URL: Repository, https://github.com/saezlab/omnipath-utils
Author-email: Denes Turei <turei.denes@gmail.com>
Maintainer-email: Denes Turei <turei.denes@gmail.com>
License-Expression: GPL-3.0-or-later
License-File: LICENSE
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Description-Content-Type: text/markdown

# omnipath-utils

ID translation, taxonomy, and reference lists for molecular biology.

[![Tests](https://github.com/saezlab/omnipath-utils/actions/workflows/ci-testing-unit.yml/badge.svg)](https://github.com/saezlab/omnipath-utils/actions)

## Quick Start

```python
from omnipath_utils.mapping import map_name, map_names
from omnipath_utils.taxonomy import ensure_ncbi_tax_id
from omnipath_utils.reflists import is_swissprot

# Translate gene symbol to UniProt
map_name('TP53', 'genesymbol', 'uniprot')
# {'P04637', ...}

# Translate multiple
map_names(['TP53', 'EGFR'], 'genesymbol', 'uniprot')
# {'P04637', 'P00533', ...}

# Resolve organism
ensure_ncbi_tax_id('human')   # 9606
ensure_ncbi_tax_id('hsapiens') # 9606

# Check if reviewed
is_swissprot('P04637')  # True
```

## Installation

```bash
pip install omnipath-utils
```

With database and web service:

```bash
pip install "omnipath-utils[server]"
```

## Web Service

```bash
omnipath-utils build --organisms 9606
omnipath-utils serve --port 8082
```

```bash
curl "http://localhost:8082/mapping/translate?identifiers=TP53,EGFR&id_type=genesymbol&target_id_type=uniprot"
```

## Documentation

https://saezlab.github.io/omnipath-utils

## License

GPL-3.0-or-later
