Closed dunleavy005 closed 6 years ago
waterer.py
partitiondriver.py
partis annotate/partition
example command: bin/partis cache-parameters --infname testing_amrit/partis_input_seqs.fa --outfname testing_amrit/partis_output.yaml --parameter-dir _output --only-smith-waterman --dont-write-parameters --dont-remove-framework-insertions --linearham
bin/partis cache-parameters --infname testing_amrit/partis_input_seqs.fa --outfname testing_amrit/partis_output.yaml --parameter-dir _output --only-smith-waterman --dont-write-parameters --dont-remove-framework-insertions --linearham
Let me know if you think the code/command should be fixed for assertions or other things.
FYI the output seems to be JSON not YAML? https://github.com/psathyrella/partis/blob/dev/python/utils.py#L3670 Doesn't matter to me either way, but the example file pasted in your docs was in YAML.
waterer.py
, no more munging withpartitiondriver.py
stuffpartis annotate/partition
too, but for linearham it's not really needed.example command:
bin/partis cache-parameters --infname testing_amrit/partis_input_seqs.fa --outfname testing_amrit/partis_output.yaml --parameter-dir _output --only-smith-waterman --dont-write-parameters --dont-remove-framework-insertions --linearham
Let me know if you think the code/command should be fixed for assertions or other things.
FYI the output seems to be JSON not YAML? https://github.com/psathyrella/partis/blob/dev/python/utils.py#L3670 Doesn't matter to me either way, but the example file pasted in your docs was in YAML.