1) --linearham mode is forced to work only with partis partition
2) --linearham mode always re-runs partis cache-parameters as loading a S-W cachefile does not allow us to get back the raw S-W data needed for flexbounds/relpos
3) wrote a utils function that writes FASTA files with the indel-reversed seqs + naive seq, which is needed for the downstream RevBayes phylogenetic inference & linearham inference
PS I used the behavior of action_cache to check whether we're in partition mode, b/c the self.current_action as documented is changing around in the script, and without this, partis tries to write FASTA files in the cache-parameter phase too.
Example command:
bin/partis partition --infname testing_amrit/partis_input_seqs.fa --outfname testing_amrit/partis_output.yaml --linearham
1) --linearham mode is forced to work only with
partis partition2) --linearham mode always re-runspartis cache-parametersas loading a S-W cachefile does not allow us to get back the raw S-W data needed for flexbounds/relpos 3) wrote autilsfunction that writes FASTA files with the indel-reversed seqs + naive seq, which is needed for the downstream RevBayes phylogenetic inference & linearham inferencePS I used the behavior of
action_cacheto check whether we're in partition mode, b/c theself.current_actionas documented is changing around in the script, and without this, partis tries to write FASTA files in thecache-parameterphase too.Example command:
bin/partis partition --infname testing_amrit/partis_input_seqs.fa --outfname testing_amrit/partis_output.yaml --linearham