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AG-1147/AG-1148/AG-1098: Add tests for rna seq data and rna distribution data #80

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merged 3 commits into from
Aug 1, 2023

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@jaclynbeck-sage jaclynbeck-sage commented Jun 29, 2023

This PR includes changes for 3 interrelated tickets:

AG-1098: The rna_distribution.py transform had 2 transforms in it (transform_rna_seq_data and transform_rna_distribution_data). The first transform is used both on its own and as a pre-requisite for the second transform. The first transform has been moved to its own file. Additionally, I renamed it (transform_rna_seq_data -> transform_rnaseq_differential_expression) to match the name that is in the config.yaml file.

AG-1147: Added a data-driven test for transform_rnaseq_differential_expression. There is a "good" input file and an input file with some missing data in each of the important columns, which should both pass. There is also a "bad" input file, where the logfc field is a string instead of a number, and this is an expected failure case.

AG-1148: Added a data-driven test for transform_rna_distribution_data. There is a "good" input file and an input file with some missing data in each of the important columns, which should both pass. There are TWO failure cases:

  1. The logfc field is a string instead of a number, which throws an error while calling transform_rnaseq_differential_expression
  2. All model entries are blank or all tissue entries are blank, which causes all rows to be dropped while calculating quartiles, and throws an error.

I made sure that both tests pass post-refactor, and that the transformed output on the real data is identical to the previous version.

@jaclynbeck-sage jaclynbeck-sage marked this pull request as ready for review June 29, 2023 16:56
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LGTM!

@jaclynbeck-sage jaclynbeck-sage merged commit df3a775 into dev Aug 1, 2023
@jaclynbeck-sage jaclynbeck-sage deleted the jbeck/AG-1147/test_transform_rna_seq branch August 1, 2023 22:02
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3 participants