Make it possible to override overlap between consecutive DNA chunks

multi_species_genomes.py

@@ -49,7 +49,6 @@ _HOMEPAGE = "https://www.ncbi.nlm.nih.gov/"
 _LICENSE = "https://www.ncbi.nlm.nih.gov/home/about/policies/"
 
 _CHUNK_LENGTHS = [6000, 12000]
-_OVERLAP = 100
 
 
 def filter_fn(char: str) -> str:
@@ -76,10 +75,11 @@ def clean_sequence(seq: str) -> str:
 class MultiSpeciesGenomesConfig(datasets.BuilderConfig):
     """BuilderConfig for The Human Reference Genome."""
 
-    def __init__(self, *args, chunk_length: int, **kwargs):
+    def __init__(self, *args, chunk_length: int, overlap: int = 100, **kwargs):
         """BuilderConfig for the multi species genomes.
         Args:
             chunk_length (:obj:`int`): Chunk length.
+            overlap: (:obj:`int`): Overlap in base pairs for two consecutive chunks (defaults to 100).
             **kwargs: keyword arguments forwarded to super.
         """
         num_kbp = int(chunk_length/1000)
@@ -89,6 +89,7 @@ class MultiSpeciesGenomesConfig(datasets.BuilderConfig):
             **kwargs,
         )
         self.chunk_length = chunk_length
+        self.overlap = overlap
 
 
 class MultiSpeciesGenomes(datasets.GeneratorBasedBuilder):
@@ -162,18 +163,18 @@ class MultiSpeciesGenomes(datasets.GeneratorBasedBuilder):
                     seq_length = len(sequence)
 
                     # split into chunks
-                    num_chunks = (seq_length - 2 * _OVERLAP) // chunk_length
+                    num_chunks = (seq_length - 2 * self.config.overlap) // chunk_length
 
                     if num_chunks < 1:
                         continue
 
-                    sequence = sequence[:(chunk_length * num_chunks + 2 * _OVERLAP)]
+                    sequence = sequence[:(chunk_length * num_chunks + 2 * self.config.overlap)]
                     seq_length = len(sequence)
 
                     for i in range(num_chunks):
                         # get chunk
                         start_pos = i * chunk_length
-                        end_pos = min(seq_length, (i+1) * chunk_length + 2 * _OVERLAP)
+                        end_pos = min(seq_length, (i+1) * chunk_length + 2 * self.config.overlap)
                         chunk_sequence = sequence[start_pos:end_pos]
 
                         # yield chunk