clinker
Both cblaster and clinker can now be used without installation on the CAGECAT webserver.
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.
A note on scope:
clinker was designed primarily as a simple way to visualise groups of homologous biosynthetic gene clusters, which are typically small genomic regions with not many genes (as in the example GIF). It performs pairwise alignments of all genes in all input files using the aligner built into BioPython, then generates an interactive SVG document in the browser. The alignment stage will scale very poorly to multiple genomes with many genes, and the resulting visualisation will also be very slow given how many SVG elements it will contain. If you are looking to align entire genomes, you will likely be better served using tools built for that purpose (e.g. Cactus).
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>
clinker can also parse GFF3 files:
clinker cluster1.gff3 cluster2.gff3 -p
Note: a corresponding FASTA file of the same name (extensions ".fa", ".fsa", ".fna", ".fasta" or ".faa") must
be found in the same directory as the GFF3, i.e. cluster1.fa and cluster2.fa.
See -h/--help for more information:
usage: clinker [-h] [--version] [-r RANGES [RANGES ...]] [-gf GENE_FUNCTIONS] [-na] [-i IDENTITY] [-j JOBS] [-s SESSION] [-ji JSON_INDENT] [-f] [-o OUTPUT] [-p [PLOT]] [-dl DELIMITER] [-dc DECIMALS] [-hl] [-ha] [-mo MATRIX_OUT] [-ufo] [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.
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
Input options:
files Gene cluster GenBank files
-r RANGES [RANGES ...], --ranges RANGES [RANGES ...]
Scaffold extraction ranges. If a range is specified, only features within the range will be extracted from the scaffold. Ranges should be formatted like: scaffold:start-end (e.g. scaffold_1:15000-40000)
-gf GENE_FUNCTIONS, --gene_functions GENE_FUNCTIONS
2-column CSV file containing gene functions, used to build gene groups from same function instead of sequence similarity (e.g. GENE_001,PKS-NRPS).
Alignment options:
-na, --no_align Do not align clusters
-i IDENTITY, --identity IDENTITY
Minimum alignment sequence identity [default: 0.3]
-j JOBS, --jobs JOBS Number of alignments to run in parallel (0 to use the number of CPUs) [default: 0]
Output options:
-s SESSION, --session SESSION
Path to clinker session
-ji JSON_INDENT, --json_indent JSON_INDENT
Number of spaces to indent JSON [default: none]
-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 [default: human readable]
-dc DECIMALS, --decimals DECIMALS
Number of decimal places in output [default: 2]
-hl, --hide_link_headers
Hide alignment column headers
-ha, --hide_aln_headers
Hide alignment cluster name headers
-mo MATRIX_OUT, --matrix_out MATRIX_OUT
Save cluster similarity matrix to file
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
Only save gene-gene links when identity is over 50%:
$ clinker files/*.gbk -i 0.5
Save an alignment session for later:
$ clinker files/*.gbk -s session.json
Save alignments to file, in comma-delimited format, with 4 decimal places:
$ clinker files/*.gbk -o alignments.csv -dl "," -dc 4
Generate visualisation:
$ clinker files/*.gbk -p
Save visualisation as a static HTML document:
$ clinker files/*.gbk -p plot.html
Cameron Gilchrist, 2020
Defining gene groups by function
By default, clinker automatically assigns a name and colour for each group of homologous genes.
You can instead pre-assign names (i.e. functions) using the -gf/--gene_functions argument, which
takes a 2-column comma-separated file like:
GENE_001,Cytochrome P450
GENE_002,Cytochrome P450
GENE_003,Methyltransferase
GENE_004,Methyltransferase
This will generate two groups, Cytochrome P450 (GENE_001 and 002), and Methyltransferase (GENE_003, GENE_004). If there any other homologous genes are identified, they will automatically be added to these groups.
As of clinker v0.0.28, you can now specify colours for genes defined by the
-gf/--gene_functions argument. To do this, use the -cm/--colour_map argument which
also takes a 2-column CSV file containing the group name and hexadecimal colour code like:
Cytochrome P450,#FF0000
Methyltransferase,#0000FF