Metadata-Version: 2.1
Name: parsomics
Version: 0.1.0
Summary: A tool for parsing omics data into a relational database
License: GPLv3
Author: Pedro Sader Azevedo
Author-email: pedro.saderazevedo@lnbr.cnpem.br
Requires-Python: >=3.12,<4.0
Classifier: License :: Other/Proprietary License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: biopython (>=1.84,<2.0)
Requires-Dist: fastapi (>=0.113.0,<0.114.0)
Requires-Dist: keyring (>=25.3.0,<26.0.0)
Requires-Dist: polars (>=1.6.0,<2.0.0)
Requires-Dist: psycopg2-binary (>=2.9.9,<3.0.0)
Requires-Dist: pydantic (>=2.9.0,<3.0.0)
Requires-Dist: sqlmodel (>=0.0.22,<0.0.23)
Requires-Dist: timeit-decorator (>=1.1.1,<2.0.0)
Description-Content-Type: text/markdown

<img align="center" height="70" src="assets/icons/icon.png">

# `parsomics`



A tool for parsing omics data into a relational database.

##  Background

The development of `parsomics` was driven by the needs of prokaryote metagenomics research, though aims to be adaptable to other studies within bioinformatics. It was created at the [Brazilian Biorenewables National Laboratory (LNBR)](https://lnbr.cnpem.br/) within the [Brazilian Center for Research in Energy](https://cnpem.br/) and Materials (CNPEM).

## Supported file formats and tools

- FASTA
- GFF
- dRep
- GTDB-Tk
- Interpro
- run_dbCAN

## Database schema

The parsomics database is structured as in the Entity-Relationship Diagram below:

![Entity-Relationship diagram of the parsomics database](assets/schema.png)

You can check out a scalable PDF version of this diagram at [assets/schema.pdf](assets/schema.pdf).

## License

This work is licensed under the terms of the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html).

