Dataset Viewer
The dataset viewer is not available for this subset.
Cannot get the split names for the config 'default' of the dataset.
Exception: SplitsNotFoundError
Message: The split names could not be parsed from the dataset config.
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 246, in _generate_tables
pa_table = paj.read_json(
^^^^^^^^^^^^^^
File "pyarrow/_json.pyx", line 342, in pyarrow._json.read_json
File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
pyarrow.lib.ArrowInvalid: JSON parse error: Column() changed from object to string in row 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 286, in get_dataset_config_info
for split_generator in builder._split_generators(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 97, in _split_generators
pa_table = next(iter(self._generate_tables(**splits[0].gen_kwargs, allow_full_read=False)))[1]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 260, in _generate_tables
batch = json_encode_fields_in_json_lines(original_batch, json_field_paths)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/utils/json.py", line 106, in json_encode_fields_in_json_lines
examples = [ujson_loads(line) for line in original_batch.splitlines()]
^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/utils/json.py", line 20, in ujson_loads
return pd.io.json.ujson_loads(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Expected object or value
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/split_names.py", line 65, in compute_split_names_from_streaming_response
for split in get_dataset_split_names(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 340, in get_dataset_split_names
info = get_dataset_config_info(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 291, in get_dataset_config_info
raise SplitsNotFoundError("The split names could not be parsed from the dataset config.") from err
datasets.inspect.SplitsNotFoundError: The split names could not be parsed from the dataset config.Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
NCBI RefSeq Protein
Normalized FASTA shards of the NCBI Reference Sequence (RefSeq) protein release.
Processed and uploaded by the MegaData post-download pipeline (internal repo). Original source: https://www.ncbi.nlm.nih.gov/refseq/.
Statistics
| Source files | 1,725 |
| Shards | 1,725 |
| Compressed shard bytes | 72.74 GiB (78,108,688,857) |
| Records (per-source manifest sum) | 459,415,871 |
| Residues (per-source manifest sum) | 179,203,453,293 |
Aggregate manifest total_records |
459415871 |
Layout
.
├── _MANIFEST.json # aggregate manifest written by the pipeline
├── manifests/<source_slug>.json # per-source manifest (records, residues, shards)
├── metadata/<source_slug>.records.jsonl # per-record provenance
└── sequences/<source_slug>/shard-NNNNNN.fasta.zst
<source_slug> corresponds 1:1 with an upstream source archive; e.g.
sequence_uniprotkb_uniprot_sprot.fasta.gz.
Loading
Stream every shard of one source (replace <source_slug> with the directory of
interest under sequences/):
hf download LiteFold/NCBI --repo-type dataset \
--include 'sequences/<source_slug>/shard-*.fasta.zst' \
--local-dir ./ncbi_refseq_protein
zstd -dc ./ncbi_refseq_protein/sequences/<source_slug>/shard-*.fasta.zst | head
Programmatic streaming with zstandard:
from huggingface_hub import snapshot_download
from pathlib import Path
import zstandard as zstd
local = snapshot_download(
repo_id="LiteFold/NCBI",
repo_type="dataset",
allow_patterns=["sequences/*/shard-*.fasta.zst"],
)
dctx = zstd.ZstdDecompressor()
for shard in sorted(Path(local).rglob("shard-*.fasta.zst")):
with shard.open("rb") as f, dctx.stream_reader(f) as reader:
buf = b""
while chunk := reader.read(1 << 20):
buf += chunk
*lines, buf = buf.split(b"\n")
for line in lines:
... # naive splitter; swap in your FASTA parser
License
Public Domain (US Government work, NCBI RefSeq policy).
Citation
O'Leary NA, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44(D1):D733-45, 2016.
Provenance
Built from the local manifest entry ncbi_refseq_protein of manifests/atlas_download_plan.json.
Pipeline source: megadata-post normalize --dataset ncbi_refseq_protein.
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