jessicaparks / SubOptLocalAlign.jl

sub-optimal local pairwise alignments and visualization

SubOptLocalAlign

Description

SubOptLocalAlign identifies sub-optimal local alignments for a pair of sequences and provides visualizations for these alignments, including a highlighted print-out of the alignments and static and interactive graphs of the alignments.

Installation

Install from the Julia REPL or from Jupyter:

using Pkg
Pkg.add(PackageSpec(url="https://github.com/jessicaparks/SubOptLocalAlign.jl"))

This assumes you already have Julia installed. Output will display best in an interactive environment, such as Jupyter Lab, which also requires IJulia.

To view the interactive graph in Jupyter, the following are also required:
(run from the terminal and refresh any open JupyterLab pages afterward)

jupyter labextension install @jupyterlab/plotly-extension
jupyter labextension install @webio/jupyter-lab-provider

Check currently installed JupyterLab extensions by:

jupyter labextension list

Usage

The main method of SubOptLocalAlign is align. See the function documentation for a complete list of arguments.

using SubOptLocalAlign

plot = SubOptLocalAlign.align("seqA.fasta", "seqB.fasta");

To use without interactive graphing, which will produce a static figure:

using SubOptLocalAlign

plot = SubOptLocalAlign.align("seqA.fasta", "seqB.fasta", figure_type="static");

Other methods can be used in cases where only subsets of the functionality are needed. See function documentation for description and arguments.