README.md

metadata

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 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.