semvec/pypi-packages huggingface dataset:
BGCfinder 0.0.30
Biosynthetic Gene Cluster finder with Graph Neural Network
License: MIT
Requires Python: >=3
Keywords: Biosynthetic Gene Cluster

# BGCfinder : Biosynthetic Gene Cluster detection with Graph Neural Network

BGCfinder detects biosynthetic gene clusters in bacterial genomes using deep learning. BGCfinder takes a fasta file containing protein sequences and convert each of them into a graph. Graph neural network takes the input graphs to detect biosynthetic gene cluster..

- Developer : Jihun Jeung (jihun@gm.gist.ac.kr, jeung4705@gmail.com)
- Github repository : https://github.com/jihunni/BGCfinder
- PyPI project website : https://pypi.org/project/BGCfinder/

Installation requirement:
- PyTorch
- PyTorch Geometric
- Prodigal (https://github.com/hyattpd/Prodigal)


To construct the conda environment,   

```bash
$ conda create --name BGCfinder  python=3.9
$ conda init bash   
$ conda activate BGCfinder   
$ conda install pytorch==1.11.0 torchvision==0.12.0 torchaudio==0.11.0 cudatoolkit=11.3 -c pytorch
$ conda install pyg -c pyg    
$ pip install BGCfinder     
```


To download the BGCfinder model and test files,   
```bash
$ bgc-download
```

To find the protein-coding gene in bacterial genome (Installation of `Prodigal` is required for this step),
```bash
$ prodigal -f gff -i bacterial_genome_seq.fasta -a bacterial_protein_seq.fasta -o bacterial_genome_seq.gff 
```

To run BGCfinder with a fasta file containing amino acid sequence with CPU (recommended),   
```bash
$ bgcfinder bacterial_protein_seq.fasta -o output_filename_prefix -l log_record.log -d False
```

To run BGCfinder with a fasta file containing amino acid sequence with GPU,   
```bash
$ bgcfinder bacterial_protein_seq.fasta -o output_filename_prefix -l log_record.log -d True
```

The development environment of BGCfinder :    
```
'torch==1.10.0',   
'torch-geometric==2.0.2',   
'torch-scatter==2.0.9',   
'torch-sparse==0.6.12'   
```
ShabiiFraction 0.0.2
Fraction by Ms.Charawi Detphumi
License: MIT
Keywords: Fraction,Mathematics

Package_name
============

ShabiiFraction is a Python library for dealing with arithmetic operation
of fractions.

Installation
------------

Use the package manager `pip <https://pip.pypa.io/en/stable/>`__ to
install ShabiiFraction.

.. code:: bash

   pip install ShabiiFraction

Usage
-----

.. code:: python

   from ShabiiFraction import Fraction

   a,b,c,d = [int(e) for e in input().split()]
   fraction1 = Fraction(a,b)
   fraction2 = Fraction(c,d)
   print(f"fraction1 = {fraction1}")
   print(f"fraction2 = {fraction2}")
   print(f"fraction1+fraction2 = {fraction1+fraction2}")
   print(f"fraction1-fraction2 = {fraction1-fraction2}")
   print(f"fraction1*fraction2 = {fraction1*fraction2}")
   print(f"fraction1/fraction2 = {fraction1/fraction2}")

Contributing
------------

Pull requests are welcome. For major changes, please open an issue first
to discuss what you would like to change.

Please make sure to update tests as appropriate.

Author
------

Charawi Detphumi

License
-------

`MIT <https://choosealicense.com/licenses/mit/>`__
akfraction 0.0.2
Fraction by Mr.Adisak
License: MIT
Keywords: Fraction,Mathematics

Package_name
============

akfraction is a Python library for dealing with arithmetic operation.

Installation
------------

Use the package manager `pip <https://pip.pypa.io/en/stable/>`__ to
install akfraction.

.. code:: bash

   pip install akfraction

Usage
-----

.. code:: python

   from akfraction import Fraction

   a,b,c,d = [int(e) for e in input().split()]
   fraction1 = Fraction(a,b)
   fraction2 = Fraction(c,d)
   print(f"fraction1 = {fraction1}")
   print(f"fraction2 = {fraction2}")
   print(f"fraction1+fraction2 = {fraction1+fraction2}")
   print(f"fraction1-fraction2 = {fraction1-fraction2}")
   print(f"fraction1*fraction2 = {fraction1*fraction2}")
   print(f"fraction1/fraction2 = {fraction1/fraction2}")

Contributing
------------

Pull requests are welcome. For major changes, please open an issue first
to discuss what you would like to change.

Please make sure to update tests as appropriate.

Author
------

Adisak Karnbanjong

License
-------

`MIT <https://choosealicense.com/licenses/mit/>`__
invenio-openaire 1.0.0a16
OpenAIRE service integration for Invenio repositories.
License: MIT
Keywords: invenio openaire

..
    This file is part of Invenio.
    Copyright (C) 2015-2019 CERN.

    Invenio is free software; you can redistribute it and/or modify it
    under the terms of the MIT License; see LICENSE file for more details.


==================
 Invenio-OpenAIRE
==================

.. image:: https://github.com/inveniosoftware/invenio-openaire/workflows/CI/badge.svg
        :target: https://github.com/inveniosoftware/invenio-openaire/actions?query=workflow%3ACI

.. image:: https://img.shields.io/coveralls/inveniosoftware/invenio-openaire.svg
        :target: https://coveralls.io/r/inveniosoftware/invenio-openaire

.. image:: https://img.shields.io/pypi/v/invenio-openaire.svg
        :target: https://pypi.org/pypi/invenio-openaire


Invenio module providing integration between Invenio repositories and OpenAIRE.

*This is an experimental developer preview release.*

* Free software: MIT license
* Documentation: https://invenio-openaire.readthedocs.io/


..
    This file is part of Invenio.
    Copyright (C) 2015-2023 CERN.

    Invenio is free software; you can redistribute it and/or modify it
    under the terms of the MIT License; see LICENSE file for more details.



Changes
=======

Version 1.0.0a16 (released 2023-03-23)

- Initial public release.