BioMCP

Feature: AlphaGenome Integration As a researcher I want to predict variant effects using AlphaGenome So that I can understand the functional impact of genetic variants Background: Given the AlphaGenome integration is available Scenario: Predict effects for a simple SNV When I request predictions for variant chr7:140753336 A>T Then the prediction should include gene expression effects And the prediction should include chromatin accessibility changes And the prediction should include a summary of affected tracks Scenario: Handle missing API key gracefully Given the ALPHAGENOME_API_KEY is not set When I request predictions for any variant Then I should receive instructions on how to obtain an API key And the response should mention that standard annotations are still available Scenario: Validate chromosome format When I request predictions for variant 23:100 A>T Then I should receive an error about invalid chromosome format And the error should specify the expected format Scenario: Validate nucleotide sequences When I request predictions for variant chr1:100 N>T Then I should receive an error about invalid nucleotides And the error should specify that only A, C, G, T are allowed Scenario: Use custom significance threshold When I request predictions for variant chr7:140753336 A>T with threshold 0.3 Then the summary should reflect the custom threshold value And more tracks should be marked as significant compared to default Scenario: Handle large genomic intervals When I request predictions with interval size 2000000 Then the system should use the maximum supported size of 1048576 And the prediction should complete successfully Scenario: Cache prediction results When I request predictions for variant chr7:140753336 A>T And I request the same prediction again Then the second request should return cached results And the response time should be significantly faster Scenario: Include tissue-specific predictions When I request predictions for variant chr7:140753336 A>T with tissue types UBERON:0002367,UBERON:0001157 Then the prediction should consider tissue-specific effects And the context should show the specified tissue types Scenario: Handle AlphaGenome API errors Given the AlphaGenome API returns an error When I request predictions for any variant Then I should receive a detailed error message And the error should include the variant context And the error should include the analysis parameters