Metadata-Version: 2.1
Name: stria
Version: 0.1.1
Summary: stria (short tandem repeat identification and analysis) is a python package for finding tandem repeats from DNA sequences
Home-page: https://github.com/lmdu/stria
Author: Lianming Du
Author-email: adullb@qq.com
License: MIT
Keywords: bioinformatics microsatellite tandem repeats
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: C
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Unix
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

stria
#####

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

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

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

*a fast Python package for identification and analysis of short tandem repeat sequences*

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

A Tandem repeat (TR) in genomic sequence is a set of adjacent short DNA sequence repeated consecutively.
The core sequence or repeat unit is generally called motif. According to the motif length, tandem repeats
can be classified as microsatellites and minisatellites. Microsatellites are also known as simple sequence
repeats (SSRs) or short tandem repeats (STRs) with motif length of 1-6 bp. Minisatellites are also sometimes
referred to as variable number of tandem repeats (VNTRs) has longer motif length than micorsatellites.

The ``stria`` is a lightweight Python C extension for identification and analysis of short tandem repeats.
The ``stria`` enables to fastly identify both exact and imperfect SSRs and VNTRs from large numbers of DNA sequences.
The ``stria`` also provides command line tools for users to extract tandem repeats from Fasta files.

Usage
=====

.. code:: python

	>>> import stria
	>>> import pyfastx
	>>> for name, seq, _ in pyfastx.Fastx('test.fa.gz'):
	>>> 	for ssr in SSRMiner(name, seq):
	>>> 		print(ssr.as_string())

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

`https://stria.readthedocs.io/ <https://stria.readthedocs.io/>`_


