clinker 0.0.5

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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 clustermap.js) 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 .

Citation

If you found clinker useful, please cite:

Gilchrist, C.L.M., Chooi, Y.-H., 2020. clinker & clustermap.js: Automatic generation of gene cluster comparison figures. bioRxiv 2020.11.08.370650. https://doi.org/10.1101/2020.11.08.370650

Usage

Running clinker can be as simple as:

clinker clusters/*.gbk

This will read in all GenBank files inside the folder, align them, and print the alignments to the terminal. To generate the visualisation, use the -p/--plot argument:

clinker clusters/*.gbk -p <optional: file name to save static HTML>

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
  -p [PLOT], --plot [PLOT]
                        Plot cluster alignments using clustermap.js. If a path
                        is given, clinker will generate a portable HTML file
                        at that path. Otherwise, the plot will be served
                        dynamically using Python's HTTP server.
  -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 -p

Cameron Gilchrist, 2020