Develop functional tests for alt_allele_prob_file and est_alt_allele_prob with multiple metafounders #156
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…prob with multiple metafounders AlphaGenes#150
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| self.output = read_and_sort_file(self.output_file_path) | ||
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| # check if the estimated alt_allele_prob is in between 0.5 and 1 (include 0.5 and exclude 1) |
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@XingerTang I have not looked at the input files, but is this what we expect for the input files - that alt allele prob will be [0.5, 1]?
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@gregorgorjanc It is specific to the test case and the test input data I designed. In general, the input values for alt allele prob should in [0, 1].
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@XingerTang I looked at these additions, but I am struggling a bit how the different input files come together what should happen and what should be the correct result and hence assert test. Can we meet at some point and discuss how to make these tests a bit more readable - maybe you just need to teach me what to look for;) |
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@gregorgorjanc Sure :) |
| # est_alt_allele_prob_single: Test the option est_alt_allele_prob | ||
| # for a single metafounder | ||
| # est_alt_allele_prob_multiple: Test the option est_alt_allele_prob | ||
| # for a single metafounder |
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@XingerTang change single here to multiple
Develop functional tests for alt_allele_prob_file and est_alt_allele_…
Feat metafounders
Commenting on Functional Tests
Test for Metafounders: single metafounder, two metafounders with separate pedigrees.
…phaPeel into feat_metafounders
Accuracy test for pedigree with two MF that cross.
1. Renamed variables MF_A to MF_A_alt_allele_prob. 2. Added code to separate the base population based on alternative allele for assignment of two metafounders in crossing pedigree (see lines 365 onwards). 3. Pushed all the simulation files as requested. 4. Minor corrections
Update in simulation data for accuracy test to incorporate multiple metafounders
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@RosCraddock can you help with R code review from @XingerTang?
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Looks good so merging this in. |
gregorgorjanc
merged commit 5189db1
into
AlphaGenes:feat_metafounders
#150
Since the main code is not updated, the test will fail.
There is some redundant/repetitive code in
test_alt_allele_prob, it will be re-organized once the main code is done.