Dataset Viewer
The dataset viewer is not available for this split.
Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code: StreamingRowsError
Exception: ReadError
Message: truncated header
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/utils.py", line 147, in get_rows_or_raise
return get_rows(
dataset=dataset,
...<4 lines>...
column_names=column_names,
)
File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
return func(*args, **kwargs)
File "/src/services/worker/src/worker/utils.py", line 127, in get_rows
rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
File "/src/services/worker/src/worker/utils.py", line 483, in safe_iter
yield from ds.decode(False) if ds.features else ds
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2951, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2471, in __iter__
for key, example in self.ex_iterable:
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 326, in __iter__
for key_example in islice(self.generate_examples_fn(**gen_kwargs), shard_example_idx_start, None):
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 127, in _generate_examples
for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
for filename, f in tar_iterator:
^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
for x in self.generator(*self.args):
~~~~~~~~~~~~~~^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1404, in _iter_from_urlpath
yield from cls._iter_tar(f)
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1355, in _iter_tar
stream = tarfile.open(fileobj=f, mode="r|*")
File "/usr/local/lib/python3.14/tarfile.py", line 1959, in open
t = cls(name, filemode, stream, **kwargs)
File "/usr/local/lib/python3.14/tarfile.py", line 1822, in __init__
self.firstmember = self.next()
~~~~~~~~~^^
File "/usr/local/lib/python3.14/tarfile.py", line 2879, in next
raise ReadError(str(e)) from None
tarfile.ReadError: truncated headerNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
S(H)ARP reference data
Reference data for S(H)ARP
(Streptomyces Hidden Antibiotic Regulated Pathways), iGEM USP-Brazil 2026.
The S(H)ARP repository does not ship these files; its scripts/fetch_data.sh
and its Colab notebook download them.
| File | Contents |
|---|---|
sharp-tmvec-cath-v1.0.tar.gz |
TM-Vec 2s index of the CATH S95 v4.4.0 domains, unpacks to sharp/data/tmvec_indexes/cath_s95.* |
sharp-tmvec-cath-v1.0.tar.gz.sha256 |
its SHA-256 checksum |
Versions
Each change to this repository is a commit. Use a URL pinned to a commit, not
to main: it always serves the same files, and the commit's date shows when
they were uploaded.
https://huggingface.co/datasets/EdwardNSeven/sharp-data/resolve/<commit>
Use
In the S(H)ARP Colab notebook, set TMVEC_INDEX_SOURCE in Advanced
parameters to the URL above. With a local install:
SHARP_DATA_SOURCE=https://huggingface.co/datasets/EdwardNSeven/sharp-data/resolve/<commit> \
scripts/fetch_data.sh --tmvec-only
Both check the archive against its .sha256 before unpacking it.
How the index was made
- Sequences:
cath-domain-seqs-S95-v4_4_0.fafrom https://download.cathdb.info/cath/releases/all-releases/v4_4_0/sequence-data/, 73,535 domains (SHA-256f93265164dc65340feebfbbffb711fe32bf326037c2bb8422f9fa432e2637387). - Model: the TM-Vec 2s student model,
tmvec2_student.pt(SHA-256fa79c537849f882a805cd583dd1022ed6c927aae55ab8ba80e89b6ad6f1ea76f), from tmvec-bench. - Command:
tmvec2s-search buildfrom S(H)ARP'ssharp/tmvec2s_search.py, with sequences over 600 residues split into overlapping windows and pooled (--long pool --overlap 200). One 512-dimension float32 vector per domain.
The S(H)ARP Colab notebook can also rebuild the index from the same sequences
(TMVEC_INDEX_SOURCE = build).
License and citation
The index is derived from CATH, which is licensed under the Creative Commons Attribution 4.0 International License.
- CATH: Waman, V. P., et al. (2025). CATH v4.4: major expansion of CATH by experimental and predicted structural data. Nucleic Acids Research, 53(D1), D348–D355. doi:10.1093/nar/gkae1087
- TM-Vec 2s: Keluskar, A., Batra, P., Bezshapkin, V., Morton, J. T., & Zhu, Q. (2026). TM-Vec 2s: Accelerated Protein Remote Homology Detection. bioRxiv. doi:10.64898/2026.02.05.704073
- TM-Vec: Hamamsy, T., et al. (2024). Protein remote homology detection and structural alignment using deep learning. Nature Biotechnology, 42(6), 975–985. doi:10.1038/s41587-023-01917-2
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