stria 0.1.3

stria (short tandem repeat identification and analysis) is a python package for finding tandem repeats from DNA sequences

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

>>> 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/