gene-cluster-matrix 0.1.0

Visualization library for gene cluster & distance

Gene Cluster Matrix

Description

Gene cluter matrix is a command line tool to generate matrix that visualize distances between genes and gene clusters. The matrix is generated as interactive html file. This tool can also visualize phylogenetic tree and phylogenetically related & unrelated gene clusters.

Gene cluster matrix is developed by Python program and distributed under the MIT license.

Dependencies

gene_cluster_matrix requires:

• python (>= 3.6)
• numpy (>= 1.20.0)
• pandas (>= 1.2.0)
• plotly (>= 5.3.0)
• gffutils (>= 0.11.0)
• toytree (>= 2.0.1)
• toyplot (>= 1.0.1)
• Pillow (>= 9.2.0)

ghostscript is required to generate phylogenetic tree image.

c.f.) Linux:sudo apt-get install ghostscript, Mac:brew install ghostscript

Install

pip install gene_cluster_matrix

Usage

• simple distance matrix

gene_cluster_matrix -g sample.gff3 -i id_list.txt -o output_name

• distance matrix with phylogenetic tree & ids in tree are mRNA

gene_cluster_matrix -g sample.gff3 -t sample.nwk -f mRNA -o output_name

• distance matrix with phylogenetic tree & clade information

gene_cluster_matrix -g sample.gff3 -t sample.nwk -c clade.csv -o output_name

Input & Option

(required)
-g or -p … GFF3 fomrat file of reference genome (gff3 file) / position data file (csv file, format should be same as sample/position.csv)
-i or -t … Gene id list ordered by your preference (txt file) / phylogenetic tree file (newick format)
-o … Output file name (string)
(optional)
-d … Threshold distance to define gene cluster (int. default=50000)
-f … Specify gff feature type (gene or mRNA) of input ids (string. default=gene)
-c … Clade information for each gene/mRNA id. (csv file. format should be same as sample/clade.csv)

Output

XXX.html or XXX_with_tree.html … interactive html file that visualize gene cluster matrix
XXX_position.csv … position data for each id in input such as id_list or tree
XXX_tree.png … phylogenetic tree figure (if -t option is used)

Example

To view the examples, clone the gene_cluster_matrix repository and run by sample data:

$ git clone https://github.com/slt666666/gene_cluster_matrix.git
$ cd gene_cluster_matrix/sample_data
$ gene_cluster_matrix -g sample.gff3 -t sample.nwk -c clade.csv -f mRNA -o test

After running above commands, html file is generated in sample_data directory.

Licence

MIT

Author

Toshiyuki Sakai