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.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
+tables/annotation_pfam_current_release_Pfam-A.regions.tsv.gz.jsonl.parts/part-00001.jsonl filter=lfs diff=lfs merge=lfs -text
+tables/annotation_pfam_current_release_Pfam-A.regions.tsv.gz.jsonl.parts/part-00000.jsonl filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,85 @@
+---
+license: cc0-1.0
+pretty_name: Pfam (Current Release)
+size_categories:
+  - 100M<n<1B
+task_categories:
+  - other
+language:
+  - en
+tags:
+  - biology
+  - proteins
+  - domains
+  - pfam
+  - annotation
+  - jsonl
+---
+
+# Pfam (Current Release)
+
+Pfam-A clans and regions tables (current release), normalized to newline-delimited JSON with row-level provenance.
+
+Processed and uploaded by the [MegaData](https://github.com/) post-download pipeline
+(internal repo). Original source: <http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/>.
+
+## Statistics
+
+| | |
+|---|---|
+| Table files | 2 |
+| Total rows | 128,220,423 |
+| Total bytes | 38.52 GiB (41,355,825,506) |
+
+## Tables
+
+| Table | Rows | Bytes |
+|---|---:|---:|
+| `annotation_pfam_current_release_Pfam-A.clans.tsv.gz.jsonl` | 27,480 | 7.00 MiB |
+| `annotation_pfam_current_release_Pfam-A.regions.tsv.gz.jsonl` | 128,192,943 | 38.51 GiB |
+
+## Layout
+
+```
+.
+├── _MANIFEST.json                 # aggregate manifest (per-table counts)
+└── tables/<source_slug>.jsonl    # normalized rows (one JSON object per line)
+```
+
+Each line in a `tables/*.jsonl` file is a JSON object with at least
+`dataset_id`, `row` (the raw upstream row), `row_index`, and `source_file`
+fields, so every row carries its upstream provenance.
+
+## Loading
+
+```bash
+hf download LiteFold/Pfam --repo-type dataset --local-dir ./pfam
+```
+
+Programmatic streaming:
+
+```python
+import json
+from pathlib import Path
+from huggingface_hub import snapshot_download
+
+local = snapshot_download(repo_id="LiteFold/Pfam", repo_type="dataset")
+for jsonl in sorted(Path(local, "tables").glob("*.jsonl")):
+    with jsonl.open() as f:
+        for line in f:
+            row = json.loads(line)
+            ...  # row["row"] is the upstream record
+```
+
+## License
+
+CC0 1.0 (EMBL-EBI Pfam).
+
+## Citation
+
+> Mistry J, et al. Pfam: The protein families database in 2021. Nucleic Acids Research, 49(D1):D412-D419, 2021.
+
+## Provenance
+
+Built from the local manifest entry `pfam` of `manifests/atlas_download_plan.json`.
+Pipeline source: `megadata-post normalize --dataset pfam --tables-only`.

_MANIFEST.json

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+{
+  "category": "domain",
+  "dataset_id": "pfam",
+  "format": "jsonl table rows with provenance",
+  "tables": [
+    {
+      "bytes": 506080,
+      "category": "domain",
+      "dataset_id": "pfam",
+      "output_file": "data/processed/domain/pfam/tables/annotation_pfam_current_release_Pfam-A.clans.tsv.gz.jsonl",
+      "rows": 27480,
+      "source_file": "annotation/pfam/current_release/Pfam-A.clans.tsv.gz",
+      "status": "ok"
+    },
+    {
+      "bytes": 5006227356,
+      "category": "domain",
+      "dataset_id": "pfam",
+      "output_file": "data/processed/domain/pfam/tables/annotation_pfam_current_release_Pfam-A.regions.tsv.gz.jsonl",
+      "rows": 128192943,
+      "source_file": "annotation/pfam/current_release/Pfam-A.regions.tsv.gz",
+      "status": "ok"
+    }
+  ],
+  "total_rows": 128220423
+}

tables/annotation_pfam_current_release_Pfam-A.regions.tsv.gz.jsonl.parts/_SPLIT_MANIFEST.json

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+  "original_name": "annotation_pfam_current_release_Pfam-A.regions.tsv.gz.jsonl",
+  "original_size": 41348483157,
+  "parts": [
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+      "size": 39999999789
+    },
+    {
+      "name": "part-00001.jsonl",
+      "size": 1348483368
+    }
+  ],
+  "tool": "gnu-split --line-bytes"
+}

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