eme_selex 0.1

Perform k-mer abundance analysis in DNA sequences

every-motif-ever

every-motif-ever (eme) is a Python package to perform k-mer abundance analysis in DNA sequences. eme is developed to perform fast and efficient analysis of short k-mers (tested with k-mers up to length 10).

While eme can be used for general purpose k-mer analysis, motivation to develop eme is to perform Systemic Evolution of Ligands by EXponential enrichment coupled with High Throughput sequencing (HT-SELEX) analysis in a Pythonic way. By default, for every k-mer, eme quantifies the fraction of reads containing that k-mer in a non-redundant manner. After the quantification, a basic position frequency matrix (PFM) for the top 50 k-mers is generated. If the user wants to generate more PFMs, they can change the top keyword argument to a desired number.

Installation

pip install https://github.com/kashyapchhatbar/every-motif-ever/archive/refs/tags/v0.1.tar.gz

Usage

Basic Usage

from eme.eme import kmer_fraction_from_file as kf

# By default, keyword arguments for size of the
# k-mer is k=5 and the number of PFMs is top=50
counts, fraction, pfm_models = kf("data/random.fa.gz")

Tutorial for HT-SELEX analysis

Jupyter notebooks detailing the usage of eme for HT-SELEX analysis are hosted on a separate repository