pegi3s/biopython_utilities repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠Biopython utilities

This Docker image contains Biopython-based scripts to perform different tasks.

⁠convert_tree.py

The convert_tree.py script allows converting between different Phylogenetic Tree formats using the Phylo module⁠.

Run the following command to show the script help: docker run --rm pegi3s/biopython_utilities convert_tree.py -h

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/biopython_utilities convert_tree.py -i /data/<input_tree> -if <input_format> -o /data/<output_tree> -of <output_format>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input phylogenetic tree you want to convert.
• <input_tree> to the actual name of your input file.
• <input_format> to the format of your input file (one of: newick, nexus, nexml, phyloxml, or cdao).
• <output_tree> to the actual name of your output file.
• <output_format> to the format of your output file (one of: newick, nexus, nexml, phyloxml, or cdao).

⁠Test data

To test this utility, the input NEXUS file is available here⁠.

⁠plot_gene_distribution.py

The plot_gene_distribution.py script represents a list of genes in a GenomeDiagram. The input data must be a TSV file with four columns: (1) the group to wich the gene belongs to (each group is drawn in a different color), (2) the name of the gene, (3) the start coordinate, and (4) the end coordinate. For instance, the test data available here⁠ contains the following 9 genes:

F-Box	Fbox1	320276	321550
F-Box	Fbox2	363707	364915
F-Box	Fbox3	473425	472151
F-Box	Fbox4	805518	807710
F-Box	Fbox5	812394	813713
F-Box	Fbox6	1542754	1541522
F-Box	Fbox7	1551260	1550496
F-Box	Fbox8	3672240	3673466
SRNase	SRNase	1545618	1547318

By default, the script:

• Represents all genes in a single horizontal line. It is possible to set the number of axis breaks with the --breaksparameter (default is 20).
• Determines the start and end positions by taking the minimum and maximum from all the genes. Nevertheless, it is possible to use the --start and --end parameters to define a custom interval.
• Represents all genes above the horizontal line. To preserve the genes strand and draw genes with start > end bellow the line, use the --preserve-strand parameter.
• Saves the figure in PDF. Use the --format to specify a different one.

Run the following command to show the script help: docker run --rm -it pegi3s/biopython_utilities plot_gene_distribution.py -h

You should adapt and run the following command: docker run --rm -it -v /your/data/dir:/data pegi3s/biopython_utilities plot_gene_distribution.py /data/<input_TSV> -o /data/<output_image>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input TSV file you want to process.
• <input_TSV> to the actual name of your input TSV file.
• <output_image> to the actual name of your output file (without the extension, which is automatically added by the script).

⁠Test data

To test this utility, the input NEXUS file is available here⁠.

⁠Changelog

The latest tag contains always the most recent version.

⁠[0.2.0] - 18/10/2021

• Add the convert_tree.py utility.

⁠[0.1.0] - 16/02/2021

• Initial biopython_utilities image containing the plot_gene_distribution.py utility.

⁠Building the image

To build this image, the version of the pegi3s/biopython image to use as base must be provided. When building from the command line, use --build-arg biopython_version=1.78.