I added in one line of code (and a few lines to save the related output file) to the pirate task to generate a gene_presence_absence.csv file that is comparable to the gene_presence_absence.csv file generated when running Roary. This allows you to use many of the post-alignment tools created for Roary on the output from Pirate (such as SCOARY, roary_plot.py, etc)
I added in one line of code (and a few lines to save the related output file) to the pirate task to generate a gene_presence_absence.csv file that is comparable to the gene_presence_absence.csv file generated when running Roary. This allows you to use many of the post-alignment tools created for Roary on the output from Pirate (such as SCOARY, roary_plot.py, etc)