| 914 | |
| 915 | class PertData: |
| 916 | def __init__(self, data_path, |
| 917 | gene_set_path=None, |
| 918 | default_pert_graph=True): |
| 919 | |
| 920 | # Dataset/Dataloader attributes |
| 921 | self.data_path = data_path |
| 922 | self.default_pert_graph = default_pert_graph |
| 923 | self.gene_set_path = gene_set_path |
| 924 | self.dataset_name = None |
| 925 | self.dataset_path = None |
| 926 | self.adata = None |
| 927 | self.dataset_processed = None |
| 928 | self.ctrl_adata = None |
| 929 | self.gene_names = [] |
| 930 | self.node_map = {} |
| 931 | |
| 932 | # Split attributes |
| 933 | self.split = None |
| 934 | self.seed = None |
| 935 | self.subgroup = None |
| 936 | self.train_gene_set_size = None |
| 937 | |
| 938 | if not os.path.exists(self.data_path): |
| 939 | os.mkdir(self.data_path) |
| 940 | server_path = 'https://dataverse.harvard.edu/api/access/datafile/6153417' |
| 941 | with open(os.path.join(self.data_path, 'gene2go_all.pkl'), 'rb') as f: |
| 942 | self.gene2go = pickle.load(f) |
| 943 | |
| 944 | def set_pert_genes(self): |
| 945 | """ |