gbouras13/pharokka

FR: add a pharokka_plotter.py argument to select the contig to be plotted in case more than one contig in the assembly

splaisan opened this issue · 2 comments

splaisan commented
  • pharokka version: 1.4.1
  • Python version: 3.10.13
  • Operating System: ubuntu 20

Description

I have a flye phage assembly which is made of a large circular contig and a left-over 10kb fragment which I do not know if it belongs to the bacteriophage or to the bacterial host.

The fragment being contig1, it gets plotted by pharokka_plotter.py by default and I do not get the map of the larger contig

What I Did

I created a separate fasta for each contig and plotted them in two runs

What I would like

either print one map for each contig to a separate picture with a clear title including the contig name
or give the user the option to specify which contig should be plotted

thanks in advance

gbouras13 commented

This is a very reasonable and useful request @splaisan - I will integrate it in the next update a make for pharokka along with some other bug fixes that have piled up (maybe in a couple of weeks).

George

splaisan commented

thanks, I guess I can close this for now
cheers