RGP borders not in regions_of_plasticity.tsv

[KerrinSteensen]

Hi,

I was using ppanggolin 1.2.105 before, and got the "start" and "stop" contig borders of the regions_of_plasticity file. With the new version (2.0.5) I only get the "start" and "stop" CDS of the borders.

example old version: region organism contig start stop genes contigBorder wholeContig strainX_contig001_RGP_14 strainX strainX_contig001 74974 86546 8 False False

example new version: region genome contig start stop genes contigBorder wholeContig strainX_contig0004_RGP_0 strainX strainX_contig0004 strainX_CDS_0254 strainX_CDS_0281 28 True True

Is there any way I can get the nucleotide borders (like in the old version)? The command I am using is : ppanggolin panrgp --fasta fastalist.txt -f --output $HOMEDIR/results/1_ppanggolin/

Thank you!

[axbazin]

Hi,

Indeed, I see where and when this change happened and I'm not 100% sure the change was voluntary, I will verify that.

In the meantime, there is no "easy" way to get that file the way you want it, but you can retrieve the info of gene starts and gene stops in any of the "genome" annotations file like gff or gene table, so it's definitely doable to write in the 'older' format with a small script.

I'll come back to this issue with the answer on whether this change was voluntary or if we'll be rolling back in futur versions.

Have a nice day, Adelme

[KerrinSteensen]

Hi Adelme,

thanks so much for your quick response and for the suggestions to find a workaround! I can already see that you started working on that issue and am looking forward to the next version of ppanggolin!

Have a good day! Kerrin

[JeanMainguy]

The fix for this issue has been released in v2.1.0.

[KerrinSteensen]

That's great. Thank you!