Develop tests for alt_allele_prob_file and est_alt_allele_prob with multiple metafounders

[XingerTang]

@RosCraddock @gregorgorjanc

Relate to #142, #149

Tasks to do:

• [x] A functional test to see if we can read alternative allele frequency and estimate the alternative allele frequency correctly for one or more than one metafounders.

Subtest Name	alt_allele_prob_file	est_alt_allele_prob	main_metafounder	Description	Complete
default	x	x	x	Test the default values of the alternative allele frequency without any input or estimation with multiple metafounders	√
alt_allele_prob_file_single	√	x	x	Test the input option alt_allele_prob_file for a single metafounder, we need the test output to be different when the alt_allele_prob_file is given	√
alt_allele_prob_file_multiple	√	x	x	Test the input option alt_allele_prob_file for multiple metafounders, we need the test output to be different when there is only a single metafounder	√
est_alt_allele_prob_single	x	√	x	Test the option est_alt_allele_prob for a single metafounder, we need a test data input such that we can infer exact alternative allele frequency from it	√
est_alt_allele_prob_multiple	x	√	x	Test the option est_alt_allele_prob for multiple metafounders, we need a test data input such that we can infer exact alternative allele frequency from it and test output to be different when there is only a single metafounder	√
both	√	√	x	Test the case when both options are used, whether the inputted alternative allele probabilities are used as a starting point for alternative allele probabilities estimation	√
incorrect_pedigree	√	x	x	Test case when a metafounder is written incorrectly as not a founder in the pedigree file	√
default_metafounder	x	x	x	Test case when 0 is being used as parents and no main metafounder is being provided as input, test whether 0 would be replaced by the default MF_1	√
main_metafounder	x	x	√	Test if the input option main_metafounder is working, requiring an input pedigree file with both metafounders and 0 as parents	√
incorrect_main_metafounder	x	x	√	Test case when the input meta_founder does not start with MF_, whether an error would be raised	√
incorrect_metafounder_in_file	√	x	x	Test case when the names of input metafounders in the input alternative allele probability file do not start with MF_, whether an error would be raised	√

• [ ] Additional accuracy tests to see if the provided/estimated alternative allele frequency can improve the accuracy:

  • [ ] a test with single metafounder and user-provided alternative allele frequency
  • [ ] a test with multiple metafounder and user-provided alternative allele frequency
  • [ ] a test with multiple metafounder and estimated alternative allele frequency

[gregorgorjanc]

Best if @RosCraddock works on this alongside you @XingerTang

[RosCraddock]

@RosCraddock @gregorgorjanc

Relate to #142, #149

Tasks to do:

• [x] A functional test to see if we can read alternative allele frequency and estimate the alternative allele frequency correctly for one or more than one metafounders.

Subtest Name alt_allele_prob_file est_alt_allele_prob main_metafounder Description Complete default x x x Test the default values of the alternative allele frequency without any input or estimation with multiple metafounders √ alt_allele_prob_file_single √ x x Test the input option alt_allele_prob_file for a single metafounder, we need the test output to be different when the alt_allele_prob_file is given √ alt_allele_prob_file_multiple √ x x Test the input option alt_allele_prob_file for multiple metafounders, we need the test output to be different when there is only a single metafounder √ est_alt_allele_prob_single x √ x Test the option est_alt_allele_prob for a single metafounder, we need a test data input such that we can infer exact alternative allele frequency from it √ est_alt_allele_prob_multiple x √ x Test the option est_alt_allele_prob for multiple metafounders, we need a test data input such that we can infer exact alternative allele frequency from it and test output to be different when there is only a single metafounder √ both √ √ x Test the case when both options are used, whether the inputted alternative allele probabilities are used as a starting point for alternative allele probabilities estimation √ incorrect_pedigree √ x x Test case when a metafounder is written incorrectly as not a founder in the pedigree file √ default_metafounder x x x Test case when 0 is being used as parents and no main metafounder is being provided as input, test whether 0 would be replaced by the default MF_1 √ main_metafounder x x √ Test if the input option main_metafounder is working, requiring an input pedigree file with both metafounders and 0 as parents √ incorrect_main_metafounder x x √ Test case when the input meta_founder does not start with MF_, whether an error would be raised √ incorrect_metafounder_in_file √ x x Test case when the names of input metafounders in the input alternative allele probability file do not start with MF_, whether an error would be raised √

• [ ] Additional accuracy tests to see if the provided/estimated alternative allele frequency can improve the accuracy:

  • [ ] a test with single metafounder and user-provided alternative allele frequency
  • [ ] a test with multiple metafounder and user-provided alternative allele frequency
  • [ ] a test with multiple metafounder and estimated alternative allele frequency

Additional Accuracy Tests:

• a test with single metafounder and user-provided alternative allele frequency
  • a test with multiple metafounder in segregated lineages and user-provided alternative allele frequency
  • a test with multiple metafounder with overlapping lineages and user-provided alternative allele frequency
  • a test with multiple metafounder in segregated lineages and estimated alternative allele frequency
  • a test with multiple metafounder iwith overlapping lineages and estimated alternative allele frequency

[XingerTang]

[like] Xinger Tang reacted to your message:

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From: Ros @.> Sent: Thursday, May 9, 2024 12:42:25 PM To: AlphaGenes/AlphaPeel @.> Cc: Xinger Tang @.>; Mention @.> Subject: Re: [AlphaGenes/AlphaPeel] Develop tests for alt_allele_prob_file and est_alt_allele_prob with multiple metafounders (Issue #150)

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@RosCraddockhttps://github.com/RosCraddock @gregorgorjanchttps://github.com/gregorgorjanc

Relate to #142https://github.com/AlphaGenes/AlphaPeel/issues/142, #149https://github.com/AlphaGenes/AlphaPeel/issues/149

Tasks to do:

• A functional test to see if we can read alternative allele frequency and estimate the alternative allele frequency correctly for one or more than one metafounders.

Subtest Name alt_allele_prob_file est_alt_allele_prob main_metafounder Description Complete default x x x Test the default values of the alternative allele frequency without any input or estimation with multiple metafounders √ alt_allele_prob_file_single √ x x Test the input option alt_allele_prob_file for a single metafounder, we need the test output to be different when the alt_allele_prob_file is given √ alt_allele_prob_file_multiple √ x x Test the input option alt_allele_prob_file for multiple metafounders, we need the test output to be different when there is only a single metafounder √ est_alt_allele_prob_single x √ x Test the option est_alt_allele_prob for a single metafounder, we need a test data input such that we can infer exact alternative allele frequency from it √ est_alt_allele_prob_multiple x √ x Test the option est_alt_allele_prob for multiple metafounders, we need a test data input such that we can infer exact alternative allele frequency from it and test output to be different when there is only a single metafounder √ both √ √ x Test the case when both options are used, whether the inputted alternative allele probabilities are used as a starting point for alternative allele probabilities estimation √ incorrect_pedigree √ x x Test case when a metafounder is written incorrectly as not a founder in the pedigree file √ default_metafounder x x x Test case when 0 is being used as parents and no main metafounder is being provided as input, test whether 0 would be replaced by the default MF_1 √ main_metafounder x x √ Test if the input option main_metafounder is working, requiring an input pedigree file with both metafounders and 0 as parents √ incorrect_main_metafounder x x √ Test case when the input metafounder does not start with MF, whether an error would be raised √ incorrect_metafounder_infile √ x x Test case when the names of input metafounders in the input alternative allele probability file do not start with MF, whether an error would be raised √

• Additional accuracy tests to see if the provided/estimated alternative allele frequency can improve the accuracy:

  • a test with single metafounder and user-provided alternative allele frequency
  • a test with multiple metafounder and user-provided alternative allele frequency
  • a test with multiple metafounder and estimated alternative allele frequency

Additional Accuracy Tests:

• a test with single metafounder and user-provided alternative allele frequency
• a test with multiple metafounder in segregated lineages and user-provided alternative allele frequency
• a test with multiple metafounder with overlapping lineages and user-provided alternative allele frequency
• a test with multiple metafounder in segregated lineages and estimated alternative allele frequency
• a test with multiple metafounder iwith overlapping lineages and estimated alternative allele frequency

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