Update jolma.py

remove deepbindweight

jolma.py

@@ -3,7 +3,7 @@ import json
 import re
 import pandas as pd
 import datasets
-
+from functools import cached_property
 
 logger = datasets.logging.get_logger(__name__)
 
@@ -54,34 +54,26 @@ _URL = "ftp://ftp.sra.ebi.ac.uk/vol1/run/"
 # _REVERSE_PRIMER = "CCTATGCGTGCTAGTGTGA"
 # _DESIGN_LENGTH = 30
 
+_DOWNLODE_MANAGER = datasets.DownloadManager()
+_RESOURCE_URL = "https://huggingface.co/datasets/thewall/DeepBindWeight/resolve/main"
+SELEX_INFO_FILE = _DOWNLODE_MANAGER.download(f"{_RESOURCE_URL}/ERP001824-deepbind.xlsx")
 
-config = datasets.load_dataset(path="thewall/deepbindweight", split="all")
-info = pd.read_excel(config['selex'][0], index_col=0)
-
-_URLS = {}
-_DESIGN_LENGTH = {}
 pattern = re.compile("(\d+)")
-for idx, row in info.iterrows():
-    sra_id = idx
-    file = row["file"]
-    _URLS[sra_id] = "/".join([_URL, sra_id[:6], sra_id, file])
-    _DESIGN_LENGTH[sra_id] = int(pattern.search(row["Ligand"]).group(0))
 
 
 class JolmaConfig(datasets.BuilderConfig):
-    def __init__(self, url, sra_id="ERR173157", length_match=True, filter_N=True, design_length=None, file=None, **kwargs):
+    def __init__(self, length_match=True, filter_N=True, **kwargs):
         super(JolmaConfig, self).__init__(**kwargs)
-        self.url = url
-        self.sra_id = sra_id
         self.length_match = length_match
-        self.design_length = design_length
         self.filter_N = filter_N
-        self.file = file
 
 
 class Jolma(datasets.GeneratorBasedBuilder):
+
+    SELEX_INFO = pd.read_excel(SELEX_INFO_FILE, index_col=0)
+
     BUILDER_CONFIGS = [
-        JolmaConfig(name=key, url=_URLS[key], design_length=_DESIGN_LENGTH[key], file=info.loc[key]['file']) for key in _URLS
+        JolmaConfig(name=index) for index in SELEX_INFO.index
     ]
 
     DEFAULT_CONFIG_NAME = "ERR173157"
@@ -101,15 +93,29 @@ class Jolma(datasets.GeneratorBasedBuilder):
             citation=_CITATION,
         )
 
+    @cached_property
+    def selex_info(self):
+        return self.SELEX_INFO.loc[self.config.name]
+
+    @cached_property
+    def design_length(self):
+        selex_info = self.selex_info
+        return int(pattern.search(selex_info["Ligand"]).group(0))
+
     def _split_generators(self, dl_manager):
         downloaded_files = None
+        sra_id = self.config.name
+        selex_info = self.selex_info
+        file = selex_info['file']
+
         if getattr(self.config, "data_dir") is not None:
-            # downloaded_files = os.path.join(self.config.data_dir, self.config.sra_id, self.config.file)
-            downloaded_files = dl_manager.extract(os.path.join(self.config.data_dir, self.config.sra_id, self.config.file))
+            path = os.path.join(self.config.data_dir, sra_id, file)
+            downloaded_files = dl_manager.extract(path)
             logger.info(f"Load from {downloaded_files}")
         if downloaded_files is None or not os.path.exists(downloaded_files):
-            logger.info(f"Download from {self.config.url}")
-            downloaded_files = dl_manager.download_and_extract(self.config.url)
+            downloaded_url = "/".join([_URL, sra_id[:6], sra_id, file])
+            logger.info(f"Download from {downloaded_url}")
+            downloaded_files = dl_manager.download_and_extract(downloaded_url)
         return [
             datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files}),
         ]
@@ -134,7 +140,7 @@ class Jolma(datasets.GeneratorBasedBuilder):
 
     def filter_fn(self, example):
         seq = example["seq"]
-        if self.config.length_match and len(seq)!=self.config.design_length:
+        if self.config.length_match and len(seq)!=self.design_length:
             return False
         if self.config.filter_N and "N" in seq:
             return False
@@ -145,5 +151,3 @@ if __name__=="__main__":
     from datasets import load_dataset
     dataset = load_dataset("jolma.py", name="ERR173157", split="all")
     # dataset = load_dataset("jolma.py", name="ERR173157", split="all", data_dir="/root/autodl-fs/ERP001824-461")
-
-