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README.md

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----
-license: mit
----
+---
+license: other
+pretty_name: NCBI RefSeq Protein
+size_categories:
+  - 100M<n<1B
+task_categories:
+  - other
+language:
+  - en
+tags:
+  - biology
+  - proteins
+  - sequences
+  - fasta
+  - refseq
+  - ncbi
+---
+
+# NCBI RefSeq Protein
+
+Normalized FASTA shards of the NCBI Reference Sequence (RefSeq) protein release.
+
+Processed and uploaded by the [MegaData](https://github.com/) 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/`):
+
+```bash
+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`](https://pypi.org/project/zstandard/):
+
+```python
+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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