Pytrf
#####
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*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.
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>`_
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"author": "Lianming Du",
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"description": "Pytrf\n#####\n\n.. image:: https://github.com/lmdu/pytrf/actions/workflows/wheel.yml/badge.svg\n :target: https://github.com/lmdu/pytrf/actions/workflows/wheel.yml\n :alt: Github Action\n\n.. image:: https://readthedocs.org/projects/pytrf/badge/?version=latest\n :target: https://pytrf.readthedocs.io/en/latest/?badge=latest\n :alt: Readthedocs\n\n.. image:: https://img.shields.io/pypi/v/pytrf.svg\n :target: https://pypi.org/project/pytrf\n :alt: PyPI\n\n.. image:: https://img.shields.io/pypi/pyversions/pytrf\n\t:target: https://pypi.org/project/pytrf\n\t:alt: PyPI\n\n.. image:: https://app.codacy.com/project/badge/Grade/bbe59e55f686465ca5824c69583e9718\n\t:target: https://app.codacy.com/gh/lmdu/pytrf/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade\n\n*a fast Python package for finding tandem repeat sequences*\n\nIntroduction\n============\n\nA Tandem repeat (TR) in genomic sequence is a set of adjacent short DNA\nsequence repeated consecutively. The pytrf is a lightweight Python C extension for identification of tandem repeats. The pytrf enables to fastly identify both exact\nor perfect SSRs. It also can find generic tandem repeats with any size of motif,\nsuch 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.\n\nUsage\n=====\n\nThe pytrf can be used as Python package. It requires `pyfastx <https://github.com/lmdu/pyfastx>`_ to parse FASTA or FASTQ file.\n\n.. code:: python\n\n\t>>> import pytrf\n\t>>> import pyfastx\n\t>>> fa = pyfastx.Fastx('test.fa', uppercase=True):\n\t>>> for name, seq in fa:\n\t>>> \tfor ssr in STRFinder(name, seq):\n\t>>> \t\tprint(ssr.as_string())\n\nCommand line\n============\n\nThe pytrf also provides command line tools for you to find tandem repeats from given FASTA or FASTQ file.\n\n.. code:: sh\n\n\tpytrf -h\n\n\tusage: pytrf command [options] fastx\n\n\ta python package for finding tandem repeats from genomic sequences\n\n\toptions:\n\t -h, --help show this help message and exit\n\t -v, --version show program's version number and exit\n\n\tcommands:\n\n\t findstr find exact or perfect short tandem repeats\n\t findgtr find exact or perfect generic tandem repeats\n\t findatr find approximate or imperfect tandem repeats\n\t extract get tandem repeat sequence and flanking sequence\n\nFor example:\n\n.. code:: sh\n\n\tpytrf findstr test.fa\n\nDocumentation\n=============\n\nFor more detailed usage, see our manual: `https://pytrf.readthedocs.io <https://pytrf.readthedocs.io>`_\n",
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