search

SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
90 stars 29 forks source link

Add minimum feature length option #53

Closed rpetit3 closed 4 years ago

rpetit3 commented 4 years ago

Hi Sion,

This is a PR related to https://github.com/SionBayliss/PIRATE/issues/51.

I've exposed the length threshold (https://github.com/SionBayliss/PIRATE/blob/master/scripts/extract_feature_sequences.pl#L41) in extract_feature_sequences.pl to the main run_PIRATE script.

I named the variable --min-length because -t was already taken and steps are put in an array named thresholds. The default value for --min-length is set to 120, same as extract_feature_sequences.pl

Tagging @plasmid02

Tim - Mind testing it out locally, and reporting back here?

Thanks!

plasmid02 commented 4 years ago

I ran using this version setting minimum length to 60 and the results looked good. Execution time not affected as far as I can tell. I did get a few "Use of initialized value" warnings - see nohup screen dump file attached

nohup.txt