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Ran 01 Oct 2024 04:01PM UTC

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Committed 01 Oct 2024 03:57PM UTC coverage: 94.523% (+0.3%) from 94.238%

Job # 11129035232.1

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push

github

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web-flow

Commit Message

Generate aafrq rscu c fmethods (#147)

- Note: all methods/tests defined in this PR precisely model the format
of methods/tests in recently approved PR [#144 for
generate_codon_frq_CFmethod](https://github.com/DuhaimeLab/VirusHostInteractionPredictor/pull/144)
- one possible area for improvement: as it stands, both
generate_codon_frq and generate_aa_frq separately populate the class
variable codon_counts. With some revision of the GeneSet class methods,
maybe this task could be isolated somehow to prevent duplication and
increased run time. Not high priority though?

Summary of this PR:
- defined the method generate_aa_frq in ComputeFeatures class to
populate class variables aa_counts and aa_frqs with dictionaries
representing amino acid -level bias of each virus and host
- defined the method generate_RSCU in ComputeFeatures class to populate
class variable RSCU with dictionaries representing bias in relative
synonymous codon usage of each virus and host
- defined pytests for both methods

---------

Co-authored-by: Eric Bastien <gbastien@umich.edu>

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