Add files using upload-large-folder tool

README.md

@@ -1,3 +1,97 @@
----
-license: mit
----
+---
+license: cc-by-4.0
+pretty_name: UniRef90
+size_categories:
+  - 100M<n<1B
+task_categories:
+  - other
+language:
+  - en
+tags:
+  - biology
+  - proteins
+  - sequences
+  - fasta
+  - uniref
+  - clustering
+---
+
+# UniRef90
+
+Normalized FASTA shards of UniRef90 cluster representative sequences (90% sequence identity threshold).
+
+Processed and uploaded by the [MegaData](https://github.com/) post-download pipeline
+(internal repo). Original source: <https://www.uniprot.org/help/uniref>.
+
+## Statistics
+
+| | |
+|---|---|
+| Source files | 1 |
+| Shards | 189 |
+| Compressed shard bytes | 38.65 GiB (41,498,595,315) |
+| Records (per-source manifest sum) | 188,848,220 |
+| Residues (per-source manifest sum) | 66,359,825,357 |
+| Aggregate manifest `total_records` | 188848220 |
+
+## 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/UniRef90 --repo-type dataset \
+  --include 'sequences/<source_slug>/shard-*.fasta.zst' \
+  --local-dir ./uniref90
+zstd -dc ./uniref90/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/UniRef90",
+    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
+
+> Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH; UniProt Consortium. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics, 31(6):926-32, 2015.
+
+## Provenance
+
+Built from the local manifest entry `uniref90` of `manifests/atlas_download_plan.json`.
+Pipeline source: `megadata-post normalize --dataset uniref90`.

_MANIFEST.json

@@ -0,0 +1,21 @@
+{
+  "dataset_id": "uniref90",
+  "format": "fasta.zst source-specific shards plus jsonl metadata",
+  "source_count": 1,
+  "sources": [
+    {
+      "dataset_id": "uniref90",
+      "format": "fasta.zst plus jsonl metadata",
+      "metadata": "data/processed/sequence/uniref90/metadata/sequence_uniref90_uniref90.fasta.gz.records.jsonl",
+      "records": 188848220,
+      "residues": 66359825357,
+      "sequence_dir": "data/processed/sequence/uniref90/sequences/sequence_uniref90_uniref90.fasta.gz",
+      "shards": 189,
+      "source_file": "sequence/uniref90/uniref90.fasta.gz",
+      "source_slug": "sequence_uniref90_uniref90.fasta.gz"
+    }
+  ],
+  "total_records": 188848220,
+  "total_residues": 66359825357,
+  "total_shards": 189
+}

manifests/sequence_uniref90_uniref90.fasta.gz.json

@@ -0,0 +1,11 @@
+{
+  "dataset_id": "uniref90",
+  "format": "fasta.zst plus jsonl metadata",
+  "metadata": "data/processed/sequence/uniref90/metadata/sequence_uniref90_uniref90.fasta.gz.records.jsonl",
+  "records": 188848220,
+  "residues": 66359825357,
+  "sequence_dir": "data/processed/sequence/uniref90/sequences/sequence_uniref90_uniref90.fasta.gz",
+  "shards": 189,
+  "source_file": "sequence/uniref90/uniref90.fasta.gz",
+  "source_slug": "sequence_uniref90_uniref90.fasta.gz"
+}

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000002.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d79d50837c7fe6ac8a7542a414364dcc68c181524dab07492c260775e9e539f1
+size 778235289

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000003.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bc6dd8f71529be1628b64b64b3a3fac036ee38f4990b01848e2cadb5430c50f1
+size 712102054

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000004.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bfc17d08d88a3363753b9b56f6820432da90cfbfa3b083319137214734a5d171
+size 650674690

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000005.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:baac06c79fe93e19bc7421e98aebb209c578befcc2121cad2cbff2d0e3f62ea9
+size 616803247

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000006.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3e89c71e6a82255f93a4530456aaeb67349d355a4440beaea4ecfd096ceb1042
+size 588878016

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000007.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3952ff57ac550d1166f2a2b7c25cdbb27cff9cd7ebc49083fa6e243af9f23bf1
+size 564165192

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000008.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a85f7422d7d33570fbf2fa2aadf06bde9a501413b506efa8b0b522b64d91d753
+size 534101744

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000009.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f9635fa150efa8a0f75d30db10270acb8f57039daf2d65330e049db3c482216d
+size 514511243

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000010.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4bb121b4e1cdc8ea21e95fb6d5d8f79ce63f16903a7daa0e0defee2c4d130f24
+size 490757677

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000011.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d74ec210669cc333fdc97374c8e39048a67e07b7e373f56fc79efef8f3193cc3
+size 477505658

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000012.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:73462ee1aad1a1c6f245ad2e9b6aa97a042985f32020f91a20255abad634d2b5
+size 465377271

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000013.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:84692ead269d565930a77834a3bd30319b46fa27d87df5db672380c61cfce791
+size 453879662

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000014.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:304267b6788bf84766879e54036ef21f79c86540467783140f64026ab5047165
+size 441492230

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000015.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eabf981ae5629aa0c84732fa9c0684ec9ffe2070f2fa89f7c8192470e787bf0e
+size 428465962

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000017.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fd00d80e1be44564e1a13f477986659cebee506a11999e8af6960c3ec409fea0
+size 409210549

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000018.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ee1bee3ce6d35e21f4f1a71cc8730d543f93d6794470d08add0551eed2bf1f39
+size 400406112

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000019.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ce8d4a6ef366d6c52e6c0bae22e9702578b9c2caab280de13b3577c7f5741b8c
+size 391613790

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000020.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3699d1f91dcedb9ff349d9ffe7f6da28e83b5e5612fd71fa3a941ff904de969a
+size 383460282

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000148.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d3dd82e0329d031e1f4efc421449bb4262fffc7f9798978ef66a8ff18959b8df
+size 106421935

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000149.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6e97e3abab10dd1a4a65d65940519fa360aae597f524bc7634c2152d66a9f5d0
+size 105171366

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000150.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:466194a466d0c1b45f5d091e5936faa93321e6daaa9afeae028b49dc6f1704e3
+size 104128919

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000151.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f0e56969fba1293538c26be92ebd8906346070ef2d3cc8914616cee4308734c7
+size 102001830

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000152.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ead7cb852b3e4efdb25820d3c59aec94e51a26ea75f5395da7037931480cd0af
+size 100763896

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000153.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8eb6c9cc1943330d385b89d6dd4d95199df53b1974cf10544ddd91c1def92288
+size 99712728

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000154.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:96e859936546e32fa9d5ace6ce55f49308201182c8c7d0230a95e9682ba4c795
+size 98561913

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000155.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8192b815efd15ef1d62eb5e0d1bd94878c5713367dd925e64d680f4a4c2380ef
+size 97114251

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000156.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bf6ae4d99d042db51000ecf233beea6072aff8155f86560c242366fb5e800ba0
+size 96337837

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000157.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:21ff226329eebb935c6533abc38d1702dcf7dde7b3799314bcc22848385dd25b
+size 94881798

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000158.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bd34af0b128130ab522f3b3cccb26cd58f2ca7bd0eb139e94995cce419da9104
+size 93440303

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000159.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4d5b4f3003114c75c136602ea355767c6bb02e61f4e5de847b6bfb5c6a0f7a46
+size 92417434

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000160.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:175e705466dbb3031aaf69ac70d43be9f699295010da8d1d04f486baf1e6a0c0
+size 90099510

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000161.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0165f83837ba1b4379b2743248997c5fda14683ccbb25fae2905d099b182bc28
+size 89140978

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000162.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:db5f188d3fb7ffbf31c69ce53be20415f496ca938456e419a20243372873d3fd
+size 88008749

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000163.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:977893fcb5ccc0335e90e0bfa154a288d98eb31554650ab2beb9a386dca02603
+size 86787435

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000164.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eab14f7bb0d85da7d97a069cf9603c52e28fbd761727a6e0a738a5796a79dd7c
+size 86047761

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000172.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:83112874878a36fa3d7871ba7bf03bc722b298ae8346c88b65a7f37e6022ba8f
+size 75269610

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000178.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9c16439fc20ae2750bd8091556f7a38255e832f9b494767068aec46a520308e9
+size 67666468

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000179.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bdb9efe1e1519f3350853858a2f9b9816739607859a1be7a4ccad26f3084c17d
+size 65571930

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000180.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cf595cbdc17ab2636aafe0c8d2f67b2e4d7f7975d087b8ac0a2314e517a0e357
+size 63881766

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000181.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eda0d4fa39b7cdfde500cb319463a1ecb06b39037dd9537b8773f05772c394ab
+size 62922260

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000182.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3e9aab1806814dc2cefc8259b680084697cf834f0378d93e414cc278cb3d8d38
+size 62700042

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000183.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:36114a7265a365dd12d8c930f781079bcb56c77a01182e47b09e3b8d195eb41c
+size 60101157

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000184.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2dc8f3ca34f0ecd38a5dbef45e438ffd8a010c7e4af2f0350ed59904ea50b03c
+size 59242284

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000185.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:15144d45d0c119cdbe1973c71d7364084ba30e1b49fdebf094a09647c551751e
+size 57402359

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000186.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:22165927f0d930e0f4b772b43f1a9015054199a5fb69ad581adbc61d77b1d594
+size 55389284

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000187.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7087642be0720d834932926b4d4be00e6113ca66c0649f6830ee94a233eb6f9a
+size 49117759

sequences/sequence_uniref90_uniref90.fasta.gz/shard-000188.fasta.zst

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4c7644d456f55438e43aecdc924c38296ff8e2587da375fa801da7413e4c842e
+size 32316710