9394625548
94%
main: 94%

Ran 06 Jun 2024 03:27AM UTC

Jobs 1

Files 8

Run time 1min

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Committed 06 Jun 2024 03:23AM UTC coverage: 93.75% (+0.07%) from 93.684%

Build # 9394625548

Build Type

push

github

Committed by

web-flow

Commit Message

Codon bias comparison class (#114)

- created CodonBiasComparison class to calculate metrics between codon
bias of a single virus GeneSet and host GeneSet
- codon bias init inputs are the dictionaries populated by any of the
GeneSet methods (i.e. codon counts, frq, aa counts, frq, RSCU)
  - defined methods for slope, R2, cosine_similarity
- wrote pytests
  - for initialization of CodonBiasComparision class
  - for all metric calculating methods in CodonBiasComparison class
- fixed a few small type inconsistencies from earlier code

- next, I will add another method to return a dataframe of the spread of
host and virus by-codon (or by-amino acid) values. This might be useful
in plotting scatterplots (and density plots!) of the distribution of
unique codon and amino acid usage by virus-host pairs.

---------

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

Run Details

465 of 496 relevant lines covered (93.75%)

1.88 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	9394625548.1	06 Jun 2024 03:27AM UTC	0	93.75	GitHub Action Run

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