Pan6461188 commited on
Commit
a8f5cc9
·
1 Parent(s): 8641604

set msa as list; label as tensor

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Files changed (1) hide show
  1. contact_prediction_binary_rag.py +19 -4
contact_prediction_binary_rag.py CHANGED
@@ -149,11 +149,12 @@ _CITATION = """
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  # You can copy an official description
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  _DESCRIPTION = """
 
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  """
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- _HOMEPAGE = "xxxxx"
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- _LICENSE = "xxxxx"
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  class DownStreamConfig(datasets.BuilderConfig):
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  """BuilderConfig for downstream taks dataset."""
@@ -176,7 +177,7 @@ class DownStreamTasks(datasets.GeneratorBasedBuilder):
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  {
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  "seq": datasets.Value("string"),
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  "label": datasets.Array2D(shape=(None, 2), dtype='int32'),
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- "msa": datasets.Value("string"),
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  "str_emb": datasets.Array2D(shape=(None, 384), dtype='float32'),
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  }
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  )
@@ -200,6 +201,7 @@ class DownStreamTasks(datasets.GeneratorBasedBuilder):
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  valid_parquet_file = dl_manager.download(f"data/valid-00000-of-00001.parquet")
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  test_parquet_file = dl_manager.download(f"data/test-00000-of-00001.parquet")
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  msa_path = dl_manager.download_and_extract(f"msa.tar")
 
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  str_file = dl_manager.download(f"md5_to_str.fasta")
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  codebook_file = dl_manager.download(f"codebook.pt")
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@@ -260,6 +262,19 @@ class DownStreamTasks(datasets.GeneratorBasedBuilder):
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  yield key, {
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  "seq": seq,
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  "label": label,
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- "msa": "|".join(msa),
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  "str_emb": str_emb
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  }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  # You can copy an official description
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  _DESCRIPTION = """
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+ Contact map prediction aims to determine whether two residues, $i$ and $j$, are in contact or not, based on their distance with a certain threshold ($<$8 Angstrom). This task is an important part of the early Alphafold version for structural prediction.
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  """
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+ _HOMEPAGE = "https://huggingface.co/datasets/genbio-ai/contact_prediction_binary_rag"
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+ _LICENSE = "Apache license 2.0"
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  class DownStreamConfig(datasets.BuilderConfig):
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  """BuilderConfig for downstream taks dataset."""
 
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  {
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  "seq": datasets.Value("string"),
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  "label": datasets.Array2D(shape=(None, 2), dtype='int32'),
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+ "msa": datasets.Sequence(datasets.Value("string")),
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  "str_emb": datasets.Array2D(shape=(None, 384), dtype='float32'),
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  }
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  )
 
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  valid_parquet_file = dl_manager.download(f"data/valid-00000-of-00001.parquet")
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  test_parquet_file = dl_manager.download(f"data/test-00000-of-00001.parquet")
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  msa_path = dl_manager.download_and_extract(f"msa.tar")
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+ # msa_path = dl_manager.download(f"msa")
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  str_file = dl_manager.download(f"md5_to_str.fasta")
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  codebook_file = dl_manager.download(f"codebook.pt")
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  yield key, {
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  "seq": seq,
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  "label": label,
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+ "msa": msa,
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  "str_emb": str_emb
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  }
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+
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+ def _as_dataset(
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+ self,
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+ split: Optional[datasets.Split] = None,
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+ **kwargs
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+ ) -> datasets.Dataset:
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+ dataset = super()._as_dataset(split=split, **kwargs)
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+ dataset.set_format(
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+ type="numpy",
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+ columns=["label", "str_emb"],
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+ output_all_columns=True
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+ )
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+ return dataset