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Project description
clinker
Gene cluster comparison figure generator
What is it?
clinker is a pipeline for easily generating publication-quality gene cluster comparison figures.
Given a set of GenBank files, clinker will automatically extract protein translations, perform global alignments between sequences in each cluster, determine the optimal display order based on cluster similarity, and generate an interactive visualisation (using ) that can be extensively tweaked before being exported as an SVG file.
Installation
clinker can be installed directly through pip:
pip install clinker
Or by cloning the source code from GitHub:
git clone https://github.com/gamcil/clinker.git
cd clinker
pip install .
Usage
Running clinker can be as simple as:
clinker clusters/*.gbk
This will run the clinker pipeline on all GenBank files within the folder and open a new tab in your web browser with the visualisation application.
See -h/--help
for more information:
usage: clinker [-h] [-i IDENTITY] [-f] [-o OUTPUT] [-dl DELIMITER]
[-dc DECIMALS] [-hl] [-ha]
files [files ...]
clinker: Automatic creation of publication-ready gene cluster comparison figures.
clinker generates gene cluster comparison figures from GenBank files.
It performs pairwise local or global alignments between every sequence
in every unique pair of clusters and generates interactive, to-scale
comparison figures using the clustermap.js library.
positional arguments:
files Gene cluster GenBank files
optional arguments:
-h, --help show this help message and exit
Alignment options:
-i IDENTITY, --identity IDENTITY
Minimum alignment sequence identity
Output options:
-f, --force Overwrite previous output file
-o OUTPUT, --output OUTPUT
Save alignments to file
-dl DELIMITER, --delimiter DELIMITER
Character to delimit output by
-dc DECIMALS, --decimals DECIMALS
Number of decimal places in output
-hl, --hide_link_headers
Hide alignment column headers
-ha, --hide_aln_headers
Hide alignment cluster name headers
Example usage
-------------
Align clusters, plot results and print scores to screen:
$ clinker files/*.gbk
Cameron Gilchrist, 2020
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