How to ask panacus just openness information

Open AndreaGuarracino opened this issue 3 months ago • 3 comments

Hi, what command should I run on a GFA to get information about opening the pangenome? I'm a bit lost about old/new documentation.

The plan is to get such info on thousands of GFA files representing HPRCv2 pangenome partitions.

Oct 06 '25 17:10 AndreaGuarracino

I am interested in the information at the top!

Oct 06 '25 17:10 AndreaGuarracino

Hi Andrea, unfortunately currently there is no command to just get the openness of the pangenome, the function is currently only part of the HTML file. However, I should be able to quickly add that information to the growth command. Let me get back to you as soon as that is implemented.

Oct 06 '25 17:10 heringerp

So I've implemented this feature now, but it is still only part of the feature branch regions. If you build this version of panacus, you can get just the alpha/growth values with

panacus growth --alpha partition.gfa | grep "alpha"

Oct 08 '25 10:10 heringerp