def train_dataloader(self):
train_dataset = TMAlignDataset(
self.hparams.train_pairs,
construct_paths=isinstance(self.loss_func, SoftPathLoss))
train_dataloader = DataLoader(
train_dataset, self.hparams.batch_size, collate_fn=collate_f,
shuffle=True, num_workers=self.hparams.num_workers,
pin_memory=True)
return train_dataloader
def test_dataloader(self):
test_dataset = TMAlignDataset(
self.hparams.test_pairs, return_names=True,
construct_paths=isinstance(self.loss_func, SoftPathLoss))
test_dataloader = DataLoader(
test_dataset, self.hparams.batch_size, shuffle=False,
collate_fn=test_collate_f, num_workers=self.hparams.num_workers,
pin_memory=True)
return test_dataloader
def val_dataloader(self):
valid_dataset = TMAlignDataset(
self.hparams.valid_pairs,
construct_paths=isinstance(self.loss_func, SoftPathLoss))
valid_dataloader = DataLoader(
valid_dataset, self.hparams.batch_size, collate_fn=collate_f,
shuffle=False, num_workers=self.hparams.num_workers,
pin_memory=True)
return valid_dataloader
def test_getitem(self):
x = TMAlignDataset(self.data_path, tm_threshold=0,
pad_ends=False, clip_ends=True)
res = x[0]
self.assertEqual(len(res), 6)
gene, pos, states, alignment_matrix, _, _ = res
# test the lengths
self.assertEqual(len(gene), 21)
self.assertEqual(len(pos), 21)
self.assertEqual(len(states), 21)
# wtf is going on here??
self.assertEqual(alignment_matrix.shape, (21, 21))
def test_gappy_getitem(self):
TMAlignDataset(self.data_path, tm_threshold=0,
pad_ends=False, clip_ends=False)
def test_constructor(self):
x = TMAlignDataset(self.data_path, tm_threshold=0, max_len=10000)
self.assertEqual(len(x), 10)