semvec/pypi-packages huggingface dataset:
scikit-ollama 0.3.2
Scikit-Ollama: an extension of Scikit-LLM for Ollama served models.
License: MIT
Requires Python: >=3.9

# Scikit-Ollama: an extension of Scikit-LLM for Ollama served models.

Leverage the power of Scikit-LLM and the security of self-hosted LLMs.

## Installation

```bash
pip install scikit-ollama
```

## Support us

You can support the project in the following ways:

- Support the original [Scikit-LLM](https://github.com/iryna-kondr/scikit-llm) package. New features will be made available downstream slowly but surely.
- Star this repository.
- Provide feedback in the [issues](<>) section.
- Share this repository with others.

## Quick start & documentation

Assuming you have installed and configured Ollama to run on your machine:

```python
from skllm.datasets import get_classification_dataset
from skollama.models.ollama.classification.zero_shot import ZeroShotOllamaClassifier

X, y = get_classification_dataset()

clf = ZeroShotOllamaClassifier(model="llama3:8b")
clf.fit(X, y)
preds = clf.predict(X)
```

For more information please refer to the [documentation](https://andreaskarasenko.github.io/skollama-docs/).

## Why Scikit-Ollama?

Scikit-Ollama lets you use locally run models for several text classification approaches.
Running models locally can be beneficial for cases where data privacy and control are paramount. This also makes you less dependent on 3rd-party APIs and gives you more control over when you want to add changes.

This project builds heavily on Scikit-LLM and has it as a core dependency. Scikit-LLM provides broad and great support to query a variety of backend families,
e.g. OpenAI, Vertex, GPT4All. In their version you could already use the OpenAI compatible v1 API backend to query locally run models. However, the issue is that Ollama does not support passing options, such as the context size to that endpoint.

Therefore this model uses the Ollama Python SDK to allow that level of control.

## Contributing

For a guide to contributing please follow the steps [here](./CONTRIBUTING.md).

## Citation

```
@software{Scikit-Ollama,
    author = {Andreas Karasenko},
    year = {2024},
    title = {Scikit-Ollama: an extension of Scikit-LLM for Ollama served models},
    url = {https://github.com/AndreasKarasenko/scikit-ollama}
}
```

If you consider citing this repository, please also consider citing `scikit-llm`.
pytrf 1.4.2
pytrf is a python package for finding tandem repeats from genomic sequences
License: MIT
Keywords: bioinformatics microsatellite tandem repeats

Pytrf
#####

.. image:: https://github.com/lmdu/pytrf/actions/workflows/wheel.yml/badge.svg
   :target: https://github.com/lmdu/pytrf/actions/workflows/wheel.yml
   :alt: Github Action

.. image:: https://readthedocs.org/projects/pytrf/badge/?version=latest
   :target: https://pytrf.readthedocs.io/en/latest/?badge=latest
   :alt: Readthedocs

.. image:: https://img.shields.io/pypi/v/pytrf.svg
   :target: https://pypi.org/project/pytrf
   :alt: PyPI

.. image:: https://img.shields.io/pypi/pyversions/pytrf
	:target: https://pypi.org/project/pytrf
	:alt: PyPI

.. image:: https://app.codacy.com/project/badge/Grade/bbe59e55f686465ca5824c69583e9718
	:target: https://app.codacy.com/gh/lmdu/pytrf/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade

*a fast Python package for finding tandem repeat sequences*

Introduction
============

A Tandem repeat (TR) in genomic sequence is a set of adjacent short DNA
sequence repeated consecutively. The pytrf is a lightweight Python C extension for identification of tandem repeats. The pytrf enables to fastly identify both exact
or perfect SSRs. It also can find generic tandem repeats with any size of motif,
such as with maximum motif length of 100 bp. Additionally, it has capability of finding approximate or imperfect tandem repeats. Furthermore, the pytrf not only can be used as Python package but also provides command line interface for users to facilitate the identification of tandem repeats.

Note: pytrf is not a Python binding to common used tool `TRF <https://tandem.bu.edu/trf/trf.html>`_.

Usage
=====

The pytrf can be used as Python package. It requires `pyfastx <https://github.com/lmdu/pyfastx>`_ to parse FASTA or FASTQ file.

.. code:: python

	>>> import pytrf
	>>> import pyfastx
	>>> fa = pyfastx.Fastx('test.fa', uppercase=True):
	>>> for name, seq in fa:
	>>> 	for ssr in STRFinder(name, seq):
	>>> 		print(ssr.as_string())

Command line
============

The pytrf also provides command line tools for you to find tandem repeats from given FASTA or FASTQ file.

.. code:: sh

	pytrf -h

	usage: pytrf command [options] fastx

	a python package for finding tandem repeats from genomic sequences

	options:
	  -h, --help     show this help message and exit
	  -v, --version  show program's version number and exit

	commands:

	    findstr      find exact or perfect short tandem repeats
	    findgtr      find exact or perfect generic tandem repeats
	    findatr      find approximate or imperfect tandem repeats
	    extract      get tandem repeat sequence and flanking sequence

For example:

.. code:: sh

	pytrf findstr test.fa

Documentation
=============

For more detailed usage, see our manual: `https://pytrf.readthedocs.io <https://pytrf.readthedocs.io>`_