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

By cloning the source code from GitHub:

git clone https://github.com/gamcil/clinker.git
cd clinker
pip install .

Or, through conda:

conda create -n clinker -c conda-forge -c bioconda clinker-py
conda activate clinker

Citation

If you found clinker useful, please cite:

clinker & clustermap.js: Automatic generation of gene cluster comparison figures.
Gilchrist, C.L.M., Chooi, Y.-H., 2020.
Bioinformatics. doi: https://doi.org/10.1093/bioinformatics/btab007

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:
  -na, --no_align       Do not align clusters
  -i IDENTITY, --identity IDENTITY
                        Minimum alignment sequence identity
  -j JOBS, --jobs JOBS  Number of alignments to run in parallel (0 to use the
                        number of CPUs)

Output options:
  -s SESSION, --session SESSION
                        Path to clinker session
  -ji JSON_INDENT, --json_indent JSON_INDENT
                        Number of spaces to indent JSON
  -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

Visualisation options:
  -ufo, --use_file_order
                        Display clusters in order of input files

Example usage
-------------
Align clusters, plot results and print scores to screen:
  $ clinker files/*.gbk -p

Cameron Gilchrist, 2020