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Datasets:
songlab
/
multiz100way

Tags:
dna
biology
genomics
License:
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The dataset viewer is not available for this dataset.
Cannot get the config names for the dataset.
Error code:   ConfigNamesError
Exception:    DataFilesNotFoundError
Message:      No (supported) data files found in songlab/multiz100way
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 67, in compute_config_names_response
                  get_dataset_config_names(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 347, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1865, in dataset_module_factory
                  raise e1 from None
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1846, in dataset_module_factory
                  return HubDatasetModuleFactoryWithoutScript(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1240, in get_module
                  module_name, default_builder_kwargs = infer_module_for_data_files(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 592, in infer_module_for_data_files
                  raise DataFilesNotFoundError("No (supported) data files found" + (f" in {path}" if path else ""))
              datasets.exceptions.DataFilesNotFoundError: No (supported) data files found in songlab/multiz100way

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Processed whole-genome alignment of 100 vertebrate species

For more information check out our paper and repository.

Source data:

Available MSAs:

  • 89.zarr.zip contains human + 89 vertebrates (excluding 10 closest primates)
  • 99.zarr.zip contains human + 99 vertebrates

Example usage:

from gpn.data import GenomeMSA

genome_msa = GenomeMSA(msa_path)
X = genome_msa.get_msa(chrom, start, end, strand="+", tokenize=False)

Coordinates:

  • hg38 assembly
  • chrom should be in ["1", "2", ..., "22", "X", "Y"]

Streaming (playing, few VEP queries)

  • Faster setup (no need to download and unzip)
  • Slower queries (depends on network connection)
  • Multiple dataloader workers don't seem to work
  • More CPU memory required to load: 10.41 GB
  • Recommended if you just want to do a few queries, e.g. VEP for a couple thousand variants
  • msa_path = "zip:///::https://huggingface.co/datasets/songlab/multiz100way/resolve/main/89.zarr.zip"

Local download (training, large-scale VEP)

  • Requires downloading (34GB) and unzipping (currently quite slow, will try to improve)
    wget https://huggingface.co/datasets/songlab/multiz100way/resolve/main/89.zarr.zip
7z x 89.zarr.zip -o89.zarr  # can still take 5 hours with 32 cores, will try to streamline this in the future
  • Update: faster unzipping here, courtesy of lpigou
  • Much faster to query
  • Can have multiple dataloader workers
  • Virtually no CPU memory required to load
  • Recommended for training or VEP for millions of variants
  • msa_path = "89.zarr"
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