Rename model-plant-reference-genome-corpus.py to arabidopsis_genome_corpus.py

model-plant-reference-genome-corpus.py → arabidopsis_genome_corpus.py

@@ -5,17 +5,13 @@ import datasets
 from Bio import SeqIO
 import os
 
-
-# Find for instance the citation on arxiv or on the dataset repo/website
 _CITATION = ""
 
-# You can copy an official description
 _DESCRIPTION = """\
 Dataset made of model plants genomes available on NCBI.
 Default configuration "6kbp" yields chunks of 6.2kbp (100bp overlap on each side). The chunks of DNA are cleaned and processed so that
 they can only contain the letters A, T, C, G and N.
 """
-
 _HOMEPAGE = "https://www.ncbi.nlm.nih.gov/"
 
 _LICENSE = "https://www.ncbi.nlm.nih.gov/home/about/policies/"
@@ -43,6 +39,7 @@ def clean_sequence(seq: str) -> str:
     seq = ''.join(list(seq))
     return seq
 
+
 class PlantSingleSpeciesGenomesConfig(datasets.BuilderConfig):
     """BuilderConfig for the Plant Single Species Pre-training Dataset."""
 
@@ -83,26 +80,17 @@ class PlantSingleSpeciesGenomes(datasets.GeneratorBasedBuilder):
             }
         )
         return datasets.DatasetInfo(
-            # This is the description that will appear on the datasets page.
             description=_DESCRIPTION,
-            # This defines the different columns of the dataset and their types
             features=features,
-            # Homepage of the dataset for documentation
             homepage=_HOMEPAGE,
-            # License for the dataset if available
             license=_LICENSE,
-            # Citation for the dataset
             citation=_CITATION,
         )
 
     def _split_generators(self, dl_manager: datasets.DownloadManager) -> List[datasets.SplitGenerator]:
-
-        filepath = dl_manager.download_and_extract('plant_genome_file_name.txt')
-        with open(filepath) as f:
-            filepath = os.path.join("plant_genomes", f.read().strip())
-
+        # A.thaliana reference genome
+        filepath = "GCF_000001735.4_TAIR10.1_genomic.fna.gz"
         downloaded_file = dl_manager.download_and_extract(filepath)
-
         return [
             datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"file": downloaded_file, "chunk_length": self.config.chunk_length})
         ]
@@ -114,8 +102,6 @@ class PlantSingleSpeciesGenomes(datasets.GeneratorBasedBuilder):
             fasta_sequences = SeqIO.parse(f, 'fasta')
 
             for record in fasta_sequences:
-
-                # parse descriptions in the fasta file
                 sequence, description = str(record.seq), record.description
 
                 # clean chromosome sequence