Move visualisation and assign query into their own programs

johnlees commented 4 years ago

Mostly moving chunks of main() around, and some changes to the command line options. Once this is finished and merged rewriting the docs (#74) will be a priority

[x] Change --fit-model to take options gmm, dbscan, refine, threshold or use
[x] Remove --full-db from assign_query
[x] Get rid of easy run
[x] Ensure return_dict = True in printExternalClusters()
[x] Check for zero sequences to remove in reference_pick.py L84-85
[x] Check that query with a single sequence works (may get zero length self dist matrix)
[x] Check assign with an older model
[x] Check visualise with an older model
[x] Check assign with a lineage model (all ranks output)
[x] Check visualise with a lineage model
[x] Visualise needs to work with assign query output. It will require update db, and should still output query/ref in the table
[x] Visualise with assigned model + lineage mode (all ranks output and #120 addressed)

Closes #77, closes #107

~NB: merge #108 and #110 first~

johnlees commented 4 years ago

97d215f804f6fc42358348e4b2078ae4c5438ac1 closes #111

johnlees commented 4 years ago

TODO: change --fit-model to take options gmm, dbscan, refine, threshold or use

johnlees commented 4 years ago

Also, remove the --full-db option from assign mode

johnlees commented 3 years ago

Suggestions addressed in #125

bacpop / PopPUNK

Move visualisation and assign query into their own programs #112