Unit tests - Githubissues

iqbal-lab-org / pling

Plasmid analysis using rearrangement distances

MIT License

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Unit tests #7

Closed babayagaofficial closed 6 months ago

babayagaofficial commented 1 year ago

Generating jaccard communities for integerisation from annotation

[x] seq_jaccard.py
[x] get_communities.py
[ ] full workflow

Integerisation from annotation

[x] rules bakta/panaroo
[x] rule gen_minimap_input
[x] consolidation.py
[x] multipartite.py
[x] blocks.py
[ ] full workflow

Integerisation from alignment

[ ] integerise_plasmids.py, unimog.py
[ ] get_communities.py
[ ] full workflow

DCJ calculation

[ ] ding output (distance matrix)
[ ] cluster_graph.py
[ ] full workflow

babayagaofficial commented 1 year ago

note that "completed" tasks in this issue mean that I have a unit test designed for a given part of the workflow, not necessarily that the test has been passed (e.g. integerise_plasmids.py has a test, but fails it due to poorly dealing with duplicates)