Update simulation.py

simulation.py

@@ -153,7 +153,7 @@ DATA_FILES = {"multiple-666": {"train": "https://huggingface.co/datasets/thewall
               }
 
 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):
+    def __init__(self, n_seq, num_motifs=1, motif_length=10, error_rate=0.0, seed=0, add_primer=False, paired=False, **kwargs):
         super(SimulationConfig, self).__init__(**kwargs)
         self.n_seq = n_seq
         self.num_motifs = num_motifs
@@ -161,19 +161,20 @@ class SimulationConfig(datasets.BuilderConfig):
         self.error_rate = error_rate
         self.seed = seed
         self.add_primer = add_primer
-        if kwargs['name']=="paired":
-            self.paired = True
-        else:
-            self.paired = False
+        self.paired = paired
+        # if "paired" in kwargs['name']:
+        #     self.paired = True
+        # else:
+        #     self.paired = False
 
 
 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, paired=True),
         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),
+        SimulationConfig(name="paired-666", n_seq=5000, seed=0, paired=True),
     ]
 
     DEFAULT_CONFIG_NAME = "multiple-666"
@@ -209,22 +210,23 @@ class Simulation(datasets.GeneratorBasedBuilder):
             ]
         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
-                          }
+                      "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,
+                      "paired": self.config.paired
+                      }
             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):
+    def _sample(self, num_motifs, motif_length, error_rate, seed, add_primer, sample_num, paired):
         simulator = SequenceGenerator(num_motifs=num_motifs, motif_length=motif_length,
                                       error_rate=error_rate, seed=seed,
-                                      add_primer=add_primer)
+                                      add_primer=add_primer, paired=paired)
         data = simulator.sample(sample_num)
         motifs = simulator.motifs
         for key, (seq, mask, motif_ids, label) in enumerate(zip(data[0], data[1], data[2], data[-1])):