eharkins
commented
4 years ago Noting that before merging I need to update the README links to point to the master branch
Closed eharkins closed 4 years ago
eharkins
commented
4 years ago Noting that before merging I need to update the README links to point to the master branch
More explicit specification of partis cluster to use for running linearham.
Read for important notes on changes introduced:
Pro: we gain the ability to specify the cluster to run on as in partis (see scripts/parse_cluster.py built to work like partis' bin/extract-fasta.py)
Con: This pull request removes the ability to run linearham with comma separated
--cluster-ind, i.e. the ability to use comma separated arguments to run the main inference part of linearham for various different clusters iteratively. This seems ok since doing so would take a long time and is still possible by writing a script to call linearham in a loop over clusters.Other important notes:
It is also still possible to specify comma-separated linearham argument
--seed-seq(maybe should be renamed to--lineage-seed-seqgiven the introduction of--partis-seed-cluster?) in order to get plots for many lineages in one cluster in a given run of linearham.This is a solution for #58 and other cases where the user is running partis separately and passing partis output, describing many clusters, to linearham and must choose one to run the linearham analysis.
cc @matsen @psathyrella