Drug-combination-synergy/datasets.py

import os.path as osp
import pandas as pd
import torch
from torch_geometric.data import Dataset, Data
import numpy as np



class DDInteractionDataset(Dataset):
    def __init__(self, root, transform=None, pre_transform=None, pre_filter=None):
        super(DDInteractionDataset, self).__init__(root, transform, pre_transform, pre_filter)

    @property
    def raw_file_names(self):
        return ['drug_interactions.tsv']

    @property
    def processed_file_names(self):
        return ['ddi_processed.pt']
    
    @property
    def raw_dir(self):
        dir = osp.join(self.root, 'raw')
        return dir

    @property
    def processed_dir(self):
        name = 'processed'
        return osp.join(self.root, name)

    def download(self):
        pass

    def process(self):
        path = osp.join(self.raw_dir, self.raw_file_names[0])
        ddi = pd.read_csv(path , sep='\t')
        edge_index = torch.tensor([ddi['drug1_idx'],ddi['drug2_idx']], dtype=torch.long)

        # ---------------------------------------------------------------
        data = Data(edge_index = edge_index)

        if self.pre_filter is not None and not self.pre_filter(data):
            pass

        if self.pre_transform is not None:
            data = self.pre_transform(data)

        torch.save(data, osp.join(self.processed_dir, 'ddi_graph_dataset.pt'))


    def len(self):
        return len(self.processed_file_names)

    def get(self):
        data = torch.load(osp.join(self.processed_dir, 'ddi_graph_dataset.pt'))
        return data


ddiDataset = DDInteractionDataset(root = "Drug/Dataset/DDI/DrugBank/")
print(ddiDataset.get().edge_index.t())