DuhaimeLab / VirusHostInteractionPredictor
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coverage: 98.649% (+0.3%) from 98.379%
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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

Relevant lines Covered
666 RELEVANT LINES 657 COVERED LINES
1.97 HITS PER LINE
Source Files on gh-readonly-queue/main/pr-186-e214bb1ce3c2793c56e10a3e0c61259635d91496

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13771228165 gh-readonly-queue/main/pr-186-e214bb1ce3c2793c56e10a3e0c61259635d91496 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 (TC... push web-flow github
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