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:

• 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:

• 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) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe. @RosCraddock<https://github.com/RosCraddock> @gregorgorjanc<https://github.com/gregorgorjanc> Relate to #142<#142>, #149<#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 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 — Reply to this email directly, view it on GitHub<#150 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMA4FSWZNPHB3ZRRSOWSMGTZBNVLDAVCNFSM6AAAAABBNGBPHKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBSGU4DQMRZGE>. You are receiving this because you were mentioned.Message ID: ***@***.***> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhun Eideann, claraichte an Alba, aireamh claraidh SC005336.