diff --git a/.gitattributes b/.gitattributes index bed0738c7eeb449bca98b5d2f33c89a1ee56349a..ee950f23d11ff26083e825b6c1067b2de9c942e7 100644 --- a/.gitattributes +++ b/.gitattributes @@ -58,3 +58,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text # Video files - compressed *.mp4 filter=lfs diff=lfs merge=lfs -text *.webm filter=lfs diff=lfs merge=lfs -text +metadata/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.records.jsonl filter=lfs diff=lfs merge=lfs -text +metadata/sequence_uniprotkb_uniprot_sprot.fasta.gz.records.jsonl filter=lfs diff=lfs merge=lfs -text diff --git a/README.md b/README.md index 7be5fc7f47d5db027d120b8024982df93db95b74..6b026e478f8312490d91832274002b17884cdab4 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,96 @@ ---- -license: mit ---- +--- +license: cc-by-4.0 +pretty_name: UniProtKB (Swiss-Prot + TrEMBL) +size_categories: + - 100M. + +## Statistics + +| | | +|---|---| +| Source files | 3 | +| Shards | 205 | +| Compressed shard bytes | 43.31 GiB (46,504,287,641) | +| Records (per-source manifest sum) | 203,172,274 | +| Residues (per-source manifest sum) | 75,747,523,712 | +| Aggregate manifest `total_records` | 203172274 | + +## Layout + +``` +. +├── _MANIFEST.json # aggregate manifest written by the pipeline +├── manifests/.json # per-source manifest (records, residues, shards) +├── metadata/.records.jsonl # per-record provenance +└── sequences//shard-NNNNNN.fasta.zst +``` + +`` corresponds 1:1 with an upstream source archive; e.g. +`sequence_uniprotkb_uniprot_sprot.fasta.gz`. + +## Loading + +Stream every shard of one source (replace `` with the directory of +interest under `sequences/`): + +```bash +hf download LiteFold/UniProtKB --repo-type dataset \ + --include 'sequences//shard-*.fasta.zst' \ + --local-dir ./uniprotkb +zstd -dc ./uniprotkb/sequences//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/UniProtKB", + 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 + +CC BY 4.0 (UniProt Consortium). + +## Citation + +> The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Research, 51(D1):D523-D531, 2023. + +## Provenance + +Built from the local manifest entry `uniprotkb` of `manifests/atlas_download_plan.json`. +Pipeline source: `megadata-post normalize --dataset uniprotkb`. diff --git a/_MANIFEST.json b/_MANIFEST.json new file mode 100644 index 0000000000000000000000000000000000000000..3045f698306543f8dec2aa7ee9b7ca4051e64cc3 --- /dev/null +++ b/_MANIFEST.json @@ -0,0 +1,43 @@ +{ + "dataset_id": "uniprotkb", + "format": "fasta.zst source-specific shards plus jsonl metadata", + "source_count": 3, + "sources": [ + { + "dataset_id": "uniprotkb", + "format": "fasta.zst plus jsonl metadata", + "metadata": "data/processed/sequence/uniprotkb/metadata/sequence_uniprotkb_uniprot_sprot.fasta.gz.records.jsonl", + "records": 574627, + "residues": 208482574, + "sequence_dir": "data/processed/sequence/uniprotkb/sequences/sequence_uniprotkb_uniprot_sprot.fasta.gz", + "shards": 1, + "source_file": "sequence/uniprotkb/uniprot_sprot.fasta.gz", + "source_slug": "sequence_uniprotkb_uniprot_sprot.fasta.gz" + }, + { + "dataset_id": "uniprotkb", + "format": "fasta.zst plus jsonl metadata", + "metadata": "data/processed/sequence/uniprotkb/metadata/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.records.jsonl", + "records": 41333, + "residues": 24903719, + "sequence_dir": "data/processed/sequence/uniprotkb/sequences/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz", + "shards": 1, + "source_file": "sequence/uniprotkb/uniprot_sprot_varsplic.fasta.gz", + "source_slug": "sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz" + }, + { + "dataset_id": "uniprotkb", + "format": "fasta.zst plus jsonl metadata", + "metadata": "data/processed/sequence/uniprotkb/metadata/sequence_uniprotkb_uniprot_trembl.fasta.gz.records.jsonl", + "records": 202556314, + "residues": 75514137419, + "sequence_dir": "data/processed/sequence/uniprotkb/sequences/sequence_uniprotkb_uniprot_trembl.fasta.gz", + "shards": 203, + "source_file": "sequence/uniprotkb/uniprot_trembl.fasta.gz", + "source_slug": "sequence_uniprotkb_uniprot_trembl.fasta.gz" + } + ], + "total_records": 203172274, + "total_residues": 75747523712, + "total_shards": 205 +} \ No newline at end of file diff --git a/manifests/sequence_uniprotkb_uniprot_sprot.fasta.gz.json b/manifests/sequence_uniprotkb_uniprot_sprot.fasta.gz.json new file mode 100644 index 0000000000000000000000000000000000000000..fc62f886fd87db49a174e0c53211183474105dd6 --- /dev/null +++ b/manifests/sequence_uniprotkb_uniprot_sprot.fasta.gz.json @@ -0,0 +1,11 @@ +{ + "dataset_id": "uniprotkb", + "format": "fasta.zst plus jsonl metadata", + "metadata": "data/processed/sequence/uniprotkb/metadata/sequence_uniprotkb_uniprot_sprot.fasta.gz.records.jsonl", + "records": 574627, + "residues": 208482574, + "sequence_dir": "data/processed/sequence/uniprotkb/sequences/sequence_uniprotkb_uniprot_sprot.fasta.gz", + "shards": 1, + "source_file": "sequence/uniprotkb/uniprot_sprot.fasta.gz", + "source_slug": "sequence_uniprotkb_uniprot_sprot.fasta.gz" +} \ No newline at end of file diff --git a/manifests/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.json b/manifests/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.json new file mode 100644 index 0000000000000000000000000000000000000000..0407896d0f42f593f3afcdb648cabdcae102ac6f --- /dev/null +++ b/manifests/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.json @@ -0,0 +1,11 @@ +{ + "dataset_id": "uniprotkb", + "format": "fasta.zst plus jsonl metadata", + "metadata": "data/processed/sequence/uniprotkb/metadata/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz.records.jsonl", + "records": 41333, + "residues": 24903719, + "sequence_dir": "data/processed/sequence/uniprotkb/sequences/sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz", + "shards": 1, + "source_file": "sequence/uniprotkb/uniprot_sprot_varsplic.fasta.gz", + "source_slug": "sequence_uniprotkb_uniprot_sprot_varsplic.fasta.gz" +} \ No newline at end of file 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