PRISM drug response metadata annotation

[Lilly-May]

PR Checklist

• Referenced issue is linked (closes Add prism sensitivity #715)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

Description of changes

• Added a method to annotate drug responses using the DepMap PRISM Repurposing 19Q4 secondary screen dose-response curve parameters.
• If multiple measurements for one cell line and drug are present, we take the mean IC50, EC50, and AUC values.
• PRISM IC50, EC50, and AUC values are stored in adata.obs.
• Added AUC annotation for GDSC data (stored in the same GDSC file we already downloaded for ln(IC50) annotation).

[Zethson]

FAILED tests/metadata/test_cell_line.py::test_gdsc_annotation - AssertionError: assert 'ln_ic50' in StrippedCellLineName perturbation ... ln_ic50_gdsc auc_gdsc\nindex ... \n0 SLR21 Midostaurin ... NaN NaN\n1 HEKTE Midostaurin ... NaN NaN\n2 TK10 Midostaurin ... -1.049992 0.814523\n3 22RV1 Midostaurin ... 1.115075 0.958313\n4 SLR21 Midostaurin ... NaN NaN\n... ... ... ... ... ...\n95 22RV1 Midostaurin ... 1.115075 0.958313\n96 SLR21 Midostaurin ... NaN NaN\n97 HEKTE Midostaurin ... NaN NaN\n98 TK10 Midostaurin ... -1.049992 0.814523\n99 22RV1 Midostaurin ... 1.115075 0.958313\n\n[100 rows x 39 columns]

• where StrippedCellLineName perturbation ... ln_ic50_gdsc auc_gdsc\nindex ... \n0 SLR21 Midostaurin ... NaN NaN\n1 HEKTE Midostaurin ... NaN NaN\n2 TK10 Midostaurin ... -1.049992 0.814523\n3 22RV1 Midostaurin ... 1.115075 0.958313\n4 SLR21 Midostaurin ... NaN NaN\n... ... ... ... ... ...\n95 22RV1 Midostaurin ... 1.115075 0.958313\n96 SLR21 Midostaurin ... NaN NaN\n97 HEKTE Midostaurin ... NaN NaN\n98 TK10 Midostaurin ... -1.049992 0.814523\n99 22RV1 Midostaurin ... 1.115075 0.958313\n\n[100 rows x 39 columns] = AnnData object with n_obs × n_vars = 100 × 100\n obs: 'StrippedCellLineName', 'perturbation', 'DepMap_ID', 'PatientID', 'CellLineName', 'DepmapModelType', 'OncotreeLineage', 'OncotreePrimaryDisease', 'OncotreeSubtype', 'OncotreeCode', 'LegacyMolecularSubtype', 'PatientMolecularSubtype', 'RRID', 'Age', 'AgeCategory', 'Sex', 'PatientRace', 'PrimaryOrMetastasis', 'SampleCollectionSite', 'SourceType', 'SourceDetail', 'TreatmentStatus', 'TreatmentDetails', 'GrowthPattern', 'OnboardedMedia', 'FormulationID', 'EngineeredModel', 'TissueOrigin', 'CCLEName', 'CatalogNumber', 'PlateCoating', 'ModelDerivationMaterial', 'PublicComments', 'WTSIMasterCellID', 'SangerModelID', 'COSMICID', 'LegacySubSubtype', 'ln_ic50_gdsc', 'auc_gdsc'\n var: 'gene_name'.obs
  FAILED tests/metadata/test_cell_line.py::test_prism_annotation - AssertionError: assert 'ic50' in DepMap_ID perturbation PatientID ... ic50_prism ec50_prism auc_prism\nindex ... \n0 ACH-000879 cytarabine PT-wMzIqz ... NaN 8.415093e+06 1.677789\n1 ACH-000488 cytarabine PT-wdkGZi ... NaN 3.891088e-02 1.200396\n2 ACH-000488 secnidazole PT-wdkGZi ... NaN 9.275898e-01 0.903011\n3 ACH-000008 flutamide PT-fp8PeY ... NaN 4.051932e-01 1.122074\n4 ACH-000879 cytarabine PT-wMzIqz ... NaN 8.415093e+06 1.677789\n... ... ... ... ... ... ... ...\n95 ACH-000008 flutamide PT-fp8PeY ... NaN 4.051932e-01 1.122074\n96 ACH-000879 cytarabine PT-wMzIqz ... NaN 8.415093e+06 1.677789\n97 ACH-000488 cytarabine PT-wdkGZi ... NaN 3.891088e-02 1.200396\n98 ACH-000488 secnidazole PT-wdkGZi ... NaN 9.275898e-01 0.903011\n99 ACH-000008 flutamide PT-fp8PeY ... NaN 4.051932e-01 1.122074\n\n[100 rows x 40 columns]
• where DepMap_ID perturbation PatientID ... ic50_prism ec50_prism auc_prism\nindex ... \n0 ACH-000879 cytarabine PT-wMzIqz ... NaN 8.415093e+06 1.677789\n1 ACH-000488 cytarabine PT-wdkGZi ... NaN 3.891088e-02 1.200396\n2 ACH-000488 secnidazole PT-wdkGZi ... NaN 9.275898e-01 0.903011\n3 ACH-000008 flutamide PT-fp8PeY ... NaN 4.051932e-01 1.122074\n4 ACH-000879 cytarabine PT-wMzIqz ... NaN 8.415093e+06 1.677789\n... ... ... ... ... ... ... ...\n95 ACH-000008 flutamide PT-fp8PeY ... NaN 4.051932e-01 1.122074\n96 ACH-000879 cytarabine PT-wMzIqz ... NaN 8.415093e+06 1.677789\n97 ACH-000488 cytarabine PT-wdkGZi ... NaN 3.891088e-02 1.200396\n98 ACH-000488 secnidazole PT-wdkGZi ... NaN 9.275898e-01 0.903011\n99 ACH-000008 flutamide PT-fp8PeY ... NaN 4.051932e-01 1.122074\n\n[100 rows x 40 columns] = AnnData object with n_obs × n_vars = 100 × 100\n obs: 'DepMap_ID', 'perturbation', 'PatientID', 'CellLineName', 'StrippedCellLineName', 'DepmapModelType', 'OncotreeLineage', 'OncotreePrimaryDisease', 'OncotreeSubtype', 'OncotreeCode', 'LegacyMolecularSubtype', 'PatientMolecularSubtype', 'RRID', 'Age', 'AgeCategory', 'Sex', 'PatientRace', 'PrimaryOrMetastasis', 'SampleCollectionSite', 'SourceType', 'SourceDetail', 'TreatmentStatus', 'TreatmentDetails', 'GrowthPattern', 'OnboardedMedia', 'FormulationID', 'EngineeredModel', 'TissueOrigin', 'CCLEName', 'CatalogNumber', 'PlateCoating', 'ModelDerivationMaterial', 'PublicComments', 'WTSIMasterCellID', 'SangerModelID', 'COSMICID', 'LegacySubSubtype', 'ic50_prism', 'ec50_prism', 'auc_prism'\n var: 'gene_name'.obs

Now the tests actually have to pass :) The CI is working again. I'll make a few changes...

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 85.18519% with 4 lines in your changes missing coverage. Please review.

Project coverage is 65.79%. Comparing base (3137547) to head (f8b6763).

Files with missing lines	Patch %	Lines
pertpy/metadata/_cell_line.py	85.18%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #716      +/-   ##
==========================================
+ Coverage   63.17%   65.79%   +2.62%     
==========================================
  Files          47       47              
  Lines        6110     6137      +27     
==========================================
+ Hits         3860     4038     +178     
+ Misses       2250     2099     -151     

Files with missing lines	Coverage Δ
pertpy/metadata/_cell_line.py	53.35% <85.18%> (+17.41%)	⬆️

... and 3 files with indirect coverage changes