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v0.2.1 - Plots and Powerpoints
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@github-actions github-actions released this 24 May 20:55
v0.2.1
c2369c7

v0.2.1

Notes

Params

  1. New optional param motifs for rule sc2rf_recombinants.
  2. New param weeks for new rule plot.
  3. Removed prev_linelist param.

Output

  1. Switch from a pdf report to powerpoint slides for better automation.
  2. Create summary plots.
  3. Split report rule into linelist and report.
  4. Output svg plots.

Workflow

  1. New rule plot.
  2. Changed growth calculation from a comparison to the previous week to a score of sequences per day.
  3. Assign a cluster_id according to the first sequence observed in the recombinant lineage.
  4. Define a recombinant lineage as a group of sequences that share the same:
    • Lineage assignment
    • Parents
    • Breakpoints or phylogenetic placement (subtree)
  5. For some sequences, the breakpoints are inaccurate and shifted slightly due to ambiguous bases. These sequences can be assigned to their corresponding cluster because they belong to the same subtree.
  6. For some lineages, global prevalence has exceeded 500 sequences (which is the subtree size used). Sequences of these lineages are split into different subtrees. However, they can be assigned to the correct cluster/lineage, because they have the same breakpoints.
  7. Confirmed not to use deletions define recombinants and breakpoints (differs from published)?

Programs

  1. Move sc2rf_recombinants.py to postprocess.py in ktmeaton fork of sc2rf.
  2. Add false positives filtering to sc2rf_recombinants based on parents and breakpoints.

Docs

  1. Add section Configuration to README.md.

Pull Requests

Commits

  • c2369c75 update CHANGELOG after README overhaul
  • 9c8a774e update autologs to exclude first blank line in notes
  • 2a8a7af5 overhaul README
  • 9c2bd2f5 change asterisks to dashes
  • 46d4ec81 update autologs to allow more complex notes content
  • a01a903c split docs into dev and todo
  • 23e8d715 change color palette for plotting
  • 785b8a19 add optional param motifs for sc2rf_recombinants
  • d1c1559e restore pptx template to regular view
  • 6adc5d32 add seaborn to environment
  • 35a04471 add changelog to report pptx
  • 99e98aa7 add epiweeks to environment
  • 1644b1fc add pptx report
  • 1ab93aff (broken) start plotting
  • 094530f0 swithc sc2rf to a postprocess script
  • 02193d6e try generalizing sc2rf post-processing
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