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- import os
-
-
- DATA_FOLDER = 'data'
- TEST_TCGA_DATA_FOLDER = os.path.join(DATA_FOLDER, 'TCGA_test_data')
- RAW_BOTH_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CTRP_GDSC_data')
- DRUG_DATA_FOLDER = os.path.join(DATA_FOLDER, 'drug_data')
- GDSC_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'GDSC_data')
- CCLE_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CCLE_data')
- GDSC_SCREENING_DATA_FOLDER = os.path.join(GDSC_RAW_DATA_FOLDER, 'drug_screening_matrix_GDSC.tsv')
- CCLE_SCREENING_DATA_FOLDER = os.path.join(CCLE_RAW_DATA_FOLDER, 'drug_screening_matrix_ccle.tsv')
- BOTH_SCREENING_DATA_FOLDER = os.path.join(RAW_BOTH_DATA_FOLDER, 'drug_screening_matrix_gdsc_ctrp.tsv')
-
- CTRP_FOLDER = os.path.join(DATA_FOLDER, 'CTRP')
- GDSC_FOLDER = os.path.join(DATA_FOLDER, 'GDSC')
- CCLE_FOLDER = os.path.join(DATA_FOLDER, 'CCLE')
-
- MODEL_FOLDER = os.path.join(DATA_FOLDER, 'model')
-
- TCGA_DATA_FOLDER = os.path.join(DATA_FOLDER, 'TCGA_data')
- TCGA_SCREENING_DATA = os.path.join(TCGA_DATA_FOLDER, 'TCGA_screening_matrix.tsv')
-
- BUILD_SIM_MATRICES = True # Make this variable True to build similarity matrices from raw data
- SIM_KERNEL = {'cell_CN': ('euclidean', 0.001), 'cell_exp': ('euclidean', 0.01), 'cell_methy': ('euclidean', 0.1),
- 'cell_mut': ('jaccard', 1), 'drug_DT': ('jaccard', 1), 'drug_comp': ('euclidean', 0.001),
- 'drug_desc': ('euclidean', 0.001), 'drug_finger': ('euclidean', 0.001)}
- SAVE_MODEL = False # Change it to True to save the trained model
- VARIATIONAL_AUTOENCODERS = False
- # DATA_MODALITIES=['cell_CN','cell_exp','cell_methy','cell_mut','drug_comp','drug_DT'] # Change this list to only consider specific data modalities
- DATA_MODALITIES = ['cell_mut', 'drug_desc', 'drug_finger']
- RANDOM_SEED = 42 # Must be used wherever can be used
-
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