Strain name changes

[drhoads]

Have run roary-scoary pipelines and now experimenting with pirate. I like the output with the percentages for each of the genes and how pirate provides more complete analysis of when an ortholog becomes a new gene. That is much more difficult with roary. My one question is why pirate is 'renaming' strains. I have quite a few genomes with names that include a hypen (-) or a period (.) and it appears that pirate is replacing them with an underscore (_). I am interested in identifying genes associated with particular traits and I need to add those trait associations but with the pirate output I have to go back in and change the strain names back.