PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
The main reason for this release is the fix in #50. Although not necessarily a problem, in some populations the reference picking step can lead the pruned network to appear inconsistent with the clusters, giving warning messages when assigning new queries. This is fixed here.
Bug fixes:
--generate-viz
mode (#44).Other:
DISPLAY
for matplotlib
The main feature added is --generate-viz
mode.
New features:
Bug fixes:
This release is mostly to create a function to assign samples, usable by an API for pathogenwatch.
New features:
Bug fixes
--use-model
modeAdding some changes and fixes that have arisen from more people testing out on their data!
New features:
--use-model
).calculate_rand_indices.py
).graphml
files for all clusters (extract_components.py
).Bug fixes:
--microreact
(#35).Other:
networkx
version for pip
(#39).This release contains an important bug fix and some changes to the output files
New features:
Bug fixes:
--full-db
) work with future --assign-query
commands (#35)Small change to setup.py
for compatibility with bioconda
This release contains features and fixes in response to review comments in the manuscript, as well as other raised issue fixes.
New features:
--external-clustering
(#30)Bug fixes:
--assign-query
(#29)New features:
--assign-query
_clusters.csv
by cluster ID, rather than sample nameBug fixes:
--update-db
works with reference only databases (#28)Bug fixes:
models.py
which causes problems with some versions of pythonBug fixes:
--assign-query
to work with inputs from non-writable directories, or directories in other locations.poppunk_references
Code:
mash.py
to utils.py