From a38a72fc16f453a0343d947e959bee4692c237f6 Mon Sep 17 00:00:00 2001 From: Hongxin <5400599+zhx828@users.noreply.github.com> Date: Tue, 14 Nov 2023 17:03:43 -0600 Subject: [PATCH] Update test_Annotation.py --- test_Annotation.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/test_Annotation.py b/test_Annotation.py index 8986fef..8e699ae 100644 --- a/test_Annotation.py +++ b/test_Annotation.py @@ -317,17 +317,17 @@ def test_fake_cna(): def check_brca2_s1882_without_cancertype(annotation, genomic_query=False): assert len(annotation) == NUMBER_OF_GC_ANNOTATION_COLUMNS if genomic_query else NUMBER_OF_ANNOTATION_COLUMNS assert annotation[( - NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + MUTATION_EFFECT_INDEX) if genomic_query else MUTATION_EFFECT_INDEX] == 'Likely Loss-of-function' + NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + MUTATION_EFFECT_INDEX) if genomic_query else MUTATION_EFFECT_INDEX] == 'Likely Loss-of-function' assert annotation[( NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + ONCOGENIC_INDEX) if genomic_query else ONCOGENIC_INDEX] == 'Likely Oncogenic' assert annotation[( - NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + HIGHEST_LEVEL_INDEX) if genomic_query else HIGHEST_LEVEL_INDEX] == 'LEVEL_1' + NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + HIGHEST_LEVEL_INDEX) if genomic_query else HIGHEST_LEVEL_INDEX] == 'LEVEL_1' assert annotation[( - NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_1_INDEX) if genomic_query else LEVEL_1_INDEX] == 'Olaparib,Olaparib+Bevacizumab,Rucaparib,Olaparib+Abiraterone+Prednisone,Niraparib,Olaparib+Abiraterone+Prednisolone,Talazoparib+Enzalutamide,Niraparib+Abiraterone Acetate+Prednisone' + NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_1_INDEX) if genomic_query else LEVEL_1_INDEX] == 'Olaparib,Olaparib+Bevacizumab,Rucaparib,Olaparib+Abiraterone+Prednisone,Niraparib,Olaparib+Abiraterone+Prednisolone,Talazoparib+Enzalutamide,Niraparib+Abiraterone Acetate+Prednisone' assert annotation[( - NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_2_INDEX) if genomic_query else LEVEL_2_INDEX] == 'Olaparib,Rucaparib,Niraparib' + NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_2_INDEX) if genomic_query else LEVEL_2_INDEX] == 'Olaparib,Rucaparib,Niraparib' assert annotation[( - NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_3A_INDEX) if genomic_query else LEVEL_3A_INDEX] == 'Olaparib,Talazoparib' + NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_3A_INDEX) if genomic_query else LEVEL_3A_INDEX] == 'Olaparib,Talazoparib' @pytest.mark.skipif(ONCOKB_API_TOKEN in (None, ''), reason="oncokb api token required")