I've now made it so we have no flexbounds/relpos values associated with 0 gene_prob as determined from the partis HMM. To do this, I check to see if the flexbounds/relpos gene names are in self.glfo['seqs'][region] for region in ['v','d','j']. From what I understand, self.glfo has a restricted set of genes that have a gene_prob > 0.
gene_probas determined from the partis HMM. To do this, I check to see if the flexbounds/relpos gene names are inself.glfo['seqs'][region]forregion in ['v','d','j']. From what I understand,self.glfohas a restricted set of genes that have agene_prob > 0.Let me know if there are mistakes in my logic.
Command:
bin/partis partition --infname testing_amrit/partis_input_seqs.fa --outfname testing_amrit/partis_output.yaml --linearham