plot_muts

Usage

You can view the usage of degen_regions via:

plot_muts --help

Example

plot_muts --refs tests/testinput/refs.fas --query tests/testinput/query.fas --out plot.png

The --out option is optional. If it is not provided, the plot will pop up on the user’s screen automatically. If this does not work, try saving the image using --out instead.

Example Output

../_images/plot_muts.png

Input File Requirements

The input must be fasta format. Both the query and ref files can have any number of sequences.

The year should be the last part of the ID, preceded by an underscore. e.g.:

>some|info|blah_blah_1995
>some_1995

If the ID uses ‘/’ rather than underscore, plot_muts currently accepts the year as the fourth field. e.g.:

>some/info/blah/1995
>some/info/blah/1995/more/info