• Home
  • Features
  • Pricing
  • Docs
  • Announcements
  • Sign In

DuhaimeLab / VirusHostInteractionPredictor / 13771228165
99%
main: 94%

Build:
Build:
LAST BUILD BRANCH: build/python-3.13
DEFAULT BRANCH: main
Ran 10 Mar 2025 05:47PM UTC
Jobs 1
Files 8
Run time 1min
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst

10 Mar 2025 05:42PM UTC coverage: 98.649% (+0.3%) from 98.379%
13771228165

push

github

web-flow
TAAI/TCAI (#186)

**components of this PR:**
- defined new class tRNAMetrics
- within tRNAMetrics class, defined virus_TAAI and virus_TCAI methods
- both methods calculate virus accordance to host tRNAs at either the
amino acid (TAAI) or codon (TCAI) levels, but both methods also include
the option to additionally calculate the virus accordance to total tRNAs
(which include viral tRNAs)
- the virus_TCAI method includes an option for skipping non-degenerate
codons (i.e. codons whose amino acids are unique to them and no other
codons)
- also restructured the tRNA frequency and count methods in the GeneSet
class to accommodate new tRNAMetrics class
- also restructured some code to reflect a more accurate amino acid list
which ignores stop codon codes
- created and updated pytests to cover all the above changes, and made
tRNA genes files more robust for testing

**ideas and issues for future:** 
- next steps: FOP (frequency of optimal codons) and incorporation of
tRNA features in ComputeFeatures class!
- mystery pytest issues (commented out for now) surrounding slope
calculation and spearman rank inverse-identical data comparison logic
- currently stop and non-degenerate codons are still counted in the
totals and therefore contribute to the divisors in codon frequency
calculations, but not for tRNA frequency. It would be nice to make this
consistent across the board.
- better handling of when viruses do not have tRNA genes...should this
impact operability of virus tRNA inclusion parameters in tRNAMetrics
methods?
- improve print statements throughout gene features workflow, keeping in
mind the anticipated throughput (i.e. print output)
- reflect more on appropriate bool defaults for including virus tRNA
genes and skipping non-degenerate codons in accordance metric
calculations

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Eric Bastien <gbastien@umich.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.nor... (continued)

657 of 666 relevant lines covered (98.65%)

1.97 hits per line

Uncovered Existing Lines

Lines Coverage ∆ File
1
99.54
0.73% vhip/mlmodel/gene_features.py
2
98.75
-0.01% vhip/mlmodel/compute_ml_features.py
Jobs
ID Job ID Ran Files Coverage
1 13771228165.1 10 Mar 2025 05:47PM UTC 16
98.65
GitHub Action Run
Source Files on build 13771228165
  • Tree
  • List 8
  • Changed 2
  • Source Changed 0
  • Coverage Changed 2
Coverage ∆ File Lines Relevant Covered Missed Hits/Line
  • Back to Repo
  • Github Actions Build #13771228165
  • b62a7b6b on github
  • Prev Build on gh-readonly-queue/main/pr-176-2d9cdcc4b0a640b6d25ce75f5c84ce8ee4c5f3ef (#12774002174)
STATUS · Troubleshooting · Open an Issue · Sales · Support · CAREERS · ENTERPRISE · START FREE · SCHEDULE DEMO
ANNOUNCEMENTS · TWITTER · TOS & SLA · Supported CI Services · What's a CI service? · Automated Testing

© 2026 Coveralls, Inc