Update simulation.py

simulation.py

@@ -146,6 +146,11 @@ class SequenceGenerator():
         return seq, new_mask, idx
 
 
+DATA_FILES = {"multiple-666": {"train": "https://huggingface.co/datasets/thewall/Simulation/resolve/main/data/multiple-666-train.parquet",
+                               "test": "https://huggingface.co/datasets/thewall/Simulation/resolve/main/data/multiple-666-test.parquet"},
+              "paired-666": {"train": "https://huggingface.co/datasets/thewall/Simulation/resolve/main/data/paired-666-train.parquet",
+                             "test": "https://huggingface.co/datasets/thewall/Simulation/resolve/main/data/paired-666-test.parquet"},
+              }
 
 class SimulationConfig(datasets.BuilderConfig):
     def __init__(self, n_seq, num_motifs=1, motif_length=10, error_rate=0.0, seed=0, add_primer=False, **kwargs):
@@ -166,10 +171,12 @@ class Simulation(datasets.GeneratorBasedBuilder):
 
     BUILDER_CONFIGS = [
         SimulationConfig(name="multiple", num_motifs=10, error_rate=0.1, n_seq=10000, seed=0),
-        SimulationConfig(name="paired", n_seq=5000, seed=0)
+        SimulationConfig(name="paired", n_seq=5000, seed=0),
+        SimulationConfig(name="multiple-666", num_motifs=10, error_rate=0.1, n_seq=10000, seed=0),
+        SimulationConfig(name="paired-666", n_seq=5000, seed=0),
     ]
 
-    DEFAULT_CONFIG_NAME = "multiple"
+    DEFAULT_CONFIG_NAME = "multiple-666"
 
     def _info(self):
         return datasets.DatasetInfo(
@@ -188,21 +195,33 @@ class Simulation(datasets.GeneratorBasedBuilder):
         )
 
     def _split_generators(self, dl_manager):
-        # downloaded_files = dl_manager.download_and_extract(self.config.url)
-        gen_kwargs = {"num_motifs": self.config.num_motifs,
-                      "motif_length": self.config.motif_length,
-                      "error_rate": self.config.error_rate,
-                      "seed": self.config.seed,
-                      "add_primer": self.config.add_primer,
-                      "sample_num": self.config.n_seq
-                      }
-        return [
-            datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs=gen_kwargs),
-        ]
-
-    def _generate_examples(self, num_motifs, motif_length, error_rate, seed, add_primer, sample_num):
-        # """This function returns the examples in the raw (text) form."""
-        # logger.info("generating examples from = %s", filepath)
+        if self.config.name in DATA_FILES:
+            train_data_file = dl_manager.download(DATA_FILES[self.config.name]['train'])
+            test_data_file = dl_manager.download(DATA_FILES[self.config.name]['train'])
+            dataset = datasets.load_dataset("parquet", data_files={"train": train_data_file,
+                                                                   "test": test_data_file})
+
+            train_iterator = self._iterator(dataset['train'])
+            test_iterator = self._iterator(dataset['test'])
+            return [
+                datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"iterator_fn": train_iterator}),
+                datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"iterator_fn": test_iterator}),
+            ]
+        else:
+            kwargs = {"num_motifs": self.config.num_motifs,
+                          "motif_length": self.config.motif_length,
+                          "error_rate": self.config.error_rate,
+                          "seed": self.config.seed,
+                          "add_primer": self.config.add_primer,
+                          "sample_num": self.config.n_seq
+                          }
+            iterator = self._sample(**kwargs)
+
+            return [
+                datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"iterator_fn": iterator}),
+            ]
+
+    def _sample(self, num_motifs, motif_length, error_rate, seed, add_primer, sample_num):
         simulator = SequenceGenerator(num_motifs=num_motifs, motif_length=motif_length,
                                       error_rate=error_rate, seed=seed,
                                       add_primer=add_primer)
@@ -216,15 +235,23 @@ class Simulation(datasets.GeneratorBasedBuilder):
                         "motif_mask": mask,
                         }
 
+    def _iterator(self, dataset):
+        for row in dataset:
+            yield row['id'], row
 
-if __name__=="__main__":
-    from datasets import load_dataset
-    dataset = load_dataset("simulation.py", name="paired", split="all")
-    print(dataset)
-    dataset = load_dataset("simulation.py", name="multiple", split="all")
-    print(dataset)
-
-    # simulator = SequenceGenerator(num_motifs=10, error_rate=0.1, seed=0)
-    # data = simulator.sample(10000)
+    def _generate_examples(self, iterator_fn):
+        yield from iterator_fn
 
 
+if __name__=="__main__":
+    from datasets import load_dataset
+    # splited_data = dataset.train_test_split(train_size=0.9, seed=666)
+    # splited_data['train'].to_parquet("paired-666-train.parquet")
+    # splited_data['test'].to_parquet("paired-666-test.parquet")
+
+    # dataset = load_dataset(path = "thewall/simulation", name="multiple", split="all")
+    # splited_data = dataset.train_test_split(train_size=0.9, seed=666)
+    # splited_data['train'].to_parquet("multiple-666-train.parquet")
+    # splited_data['test'].to_parquet("multiple-666-test.parquet")
+    
+    dataset = load_dataset("simulation.py", name="paired-666", split="test")