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- .gitattributes +381 -35
- README.md +86 -0
- README_zh.md +86 -0
- fasttrans-client.tar.gz +3 -0
- fasttrans/install_rayfile.sh +14 -0
- fasttrans/rayfile-c +3 -0
- fasttrans/readme.txt +5 -0
- manifest.yaml +291 -0
- metadata/file_manifest.yaml +0 -0
- metadata/schema.yaml +71 -0
- onescience_run_manifest.yaml +291 -0
- reference/HOMO_SAPIENS/GRCh38.p13.genome.fa +3 -0
- reference/HOMO_SAPIENS/GRCh38.p13.genome.fa.fai +639 -0
- reference/HOMO_SAPIENS/gencode.v46.annotation.gtf.gz.feather +3 -0
- reference/HOMO_SAPIENS/gencode.v46.splice_sites_ends.feather +3 -0
- reference/HOMO_SAPIENS/gencode.v46.splice_sites_starts.feather +3 -0
- reference/HOMO_SAPIENS/polyadb_human_v3_exon3_contiguous_gtfv46.feather +3 -0
- reference/MUS_MUSCULUS/GRCm38.p6.genome.fa +3 -0
- reference/MUS_MUSCULUS/GRCm38.p6.genome.fa.fai +139 -0
- reference/MUS_MUSCULUS/gencode.vM23.annotation.gtf.gz.feather +3 -0
- reference/MUS_MUSCULUS/gencode.vM38.splice_sites_ends.feather +3 -0
- reference/MUS_MUSCULUS/gencode.vM38.splice_sites_starts.feather +3 -0
- scripts/validate_dataset.py +79 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_01-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_02-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_03-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_04-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_05-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_06-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_07-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_08-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_09-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_10-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_11-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_12-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_13-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_14-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_15-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_16-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_17-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_18-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_19-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_20-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_21-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_22-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_23-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_24-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_25-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/CAGE/data_chrAll_01-25.gz.tfrecord +3 -0
- v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/CAGE/data_chrAll_02-25.gz.tfrecord +3 -0
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| 329 |
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| 330 |
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| 331 |
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| 332 |
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| 333 |
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| 334 |
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| 335 |
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| 338 |
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| 342 |
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| 343 |
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| 356 |
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| 357 |
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| 358 |
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| 366 |
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| 391 |
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| 392 |
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| 399 |
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README.md
ADDED
|
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|
| 1 |
+
---
|
| 2 |
+
license: other
|
| 3 |
+
tags:
|
| 4 |
+
- GRCh38
|
| 5 |
+
- GRCm38
|
| 6 |
+
language:
|
| 7 |
+
- en
|
| 8 |
+
- zh
|
| 9 |
+
---
|
| 10 |
+
<p align="center">
|
| 11 |
+
<strong>
|
| 12 |
+
<span style="font-size: 30px;">AlphaGenome Dataset</span>
|
| 13 |
+
</strong>
|
| 14 |
+
</p>
|
| 15 |
+
|
| 16 |
+
## Dataset Description
|
| 17 |
+
|
| 18 |
+
AlphaGenome Dataset is a curated package of reference genomes, annotation files, and TFRecord data for use with the OneScience AlphaGenome model.
|
| 19 |
+
|
| 20 |
+
The reference resources include human GRCh38.p13, mouse GRCm38.p6, FAI indexes, Gencode annotations, splice-site annotations, and polyA annotations. The TFRecord data contains 12 bundles from the HOMO_SAPIENS VALID split, with 25 gzip-compressed shards in each bundle.
|
| 21 |
+
|
| 22 |
+
## Supported Tasks
|
| 23 |
+
|
| 24 |
+
This dataset has been adapted for `OneScience/alphagenome/`. By default, the model repository expects this dataset to be located at `data/alphagenome_dataset` within the model package. It is used for preflight checks, interval inference, variant scoring, and track-prediction evaluation.
|
| 25 |
+
|
| 26 |
+
## Dataset Format and Structure
|
| 27 |
+
|
| 28 |
+
TFRecord file paths follow this pattern:
|
| 29 |
+
|
| 30 |
+
```text
|
| 31 |
+
v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/<BUNDLE>/data_chrAll_01-25.gz.tfrecord
|
| 32 |
+
```
|
| 33 |
+
|
| 34 |
+
The bundles comprise ATAC, DNASE, PROCAP, CAGE, RNA_SEQ, CHIP_TF, CHIP_HISTONE, CONTACT_MAPS, SPLICE_SITES, SPLICE_SITE_USAGE, SPLICE_JUNCTIONS, and SPLICE_SITE_POSITIONS. Each sample contains a DNA sequence, interval chromosome/start/end metadata, a target tensor, and a mask; see `metadata/schema.yaml` for dtype and resolution.
|
| 35 |
+
|
| 36 |
+
## How to Use the Dataset
|
| 37 |
+
|
| 38 |
+
### Files and Download
|
| 39 |
+
|
| 40 |
+
Standalone download:
|
| 41 |
+
|
| 42 |
+
```bash
|
| 43 |
+
hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir .
|
| 44 |
+
```
|
| 45 |
+
|
| 46 |
+
Use within the model package:
|
| 47 |
+
|
| 48 |
+
```bash
|
| 49 |
+
hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir data/alphagenome_dataset
|
| 50 |
+
```
|
| 51 |
+
|
| 52 |
+
### Data Placement and Validation
|
| 53 |
+
|
| 54 |
+
When used as a model dependency, the following directory structure is recommended:
|
| 55 |
+
|
| 56 |
+
```text
|
| 57 |
+
<model-package>/data/alphagenome_dataset/
|
| 58 |
+
├── manifest.yaml
|
| 59 |
+
├── metadata/
|
| 60 |
+
├── reference/
|
| 61 |
+
└── v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 62 |
+
```
|
| 63 |
+
|
| 64 |
+
Quickly validate file presence, sizes, and gzip readability:
|
| 65 |
+
|
| 66 |
+
```bash
|
| 67 |
+
python scripts/validate_dataset.py --root .
|
| 68 |
+
```
|
| 69 |
+
|
| 70 |
+
Add `--check-sha256` to perform a complete SHA256 validation.
|
| 71 |
+
|
| 72 |
+
## Official OneScience Information
|
| 73 |
+
|
| 74 |
+
| Platform | OneScience Main Repository | Skills Repository |
|
| 75 |
+
|---|---|---|
|
| 76 |
+
| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
|
| 77 |
+
| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |
|
| 78 |
+
|
| 79 |
+
## Limitations and License
|
| 80 |
+
|
| 81 |
+
license: mixed
|
| 82 |
+
license_note: >
|
| 83 |
+
AlphaGenome training, validation and test datasets contain reprocessed
|
| 84 |
+
data from FANTOM5, 4D Nucleome, ENCODE and GENCODE. Usage is subject
|
| 85 |
+
to the respective source-specific licenses and data-use policies.
|
| 86 |
+
Other unspecified materials are licensed under CC BY-NC 4.0.
|
README_zh.md
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: other
|
| 3 |
+
tags:
|
| 4 |
+
- GRCh38
|
| 5 |
+
- GRCm38
|
| 6 |
+
language:
|
| 7 |
+
- en
|
| 8 |
+
- zh
|
| 9 |
+
---
|
| 10 |
+
<p align="center">
|
| 11 |
+
<strong>
|
| 12 |
+
<span style="font-size: 30px;">AlphaGenome Dataset</span>
|
| 13 |
+
</strong>
|
| 14 |
+
</p>
|
| 15 |
+
|
| 16 |
+
## 数据集描述
|
| 17 |
+
|
| 18 |
+
AlphaGenome Dataset 是供 OneScience AlphaGenome 模型使用的参考基因组、注释文件和 TFRecord 数据整理包。
|
| 19 |
+
|
| 20 |
+
参考资源包括人类 GRCh38.p13、小鼠 GRCm38.p6、FAI 索引、Gencode 注释、剪接位点和 polyA 注释；TFRecord 数据包含 HOMO_SAPIENS VALID split 的 12 个 bundle，每个 bundle 25 个 gzip 压缩分片。
|
| 21 |
+
|
| 22 |
+
## 数据集支持的任务
|
| 23 |
+
|
| 24 |
+
本数据集适配 `OneScience/alphagenome/`。模型仓库默认期望本数据集位于模型包 `data/alphagenome_dataset`，用于预检、区间推理、变异评分和轨迹预测评测。
|
| 25 |
+
|
| 26 |
+
## 数据集的格式和结构
|
| 27 |
+
|
| 28 |
+
TFRecord 文件路径形如：
|
| 29 |
+
|
| 30 |
+
```text
|
| 31 |
+
v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/<BUNDLE>/data_chrAll_01-25.gz.tfrecord
|
| 32 |
+
```
|
| 33 |
+
|
| 34 |
+
Bundle 包括 ATAC、DNASE、PROCAP、CAGE、RNA_SEQ、CHIP_TF、CHIP_HISTONE、CONTACT_MAPS、SPLICE_SITES、SPLICE_SITE_USAGE、SPLICE_JUNCTIONS 和 SPLICE_SITE_POSITIONS。每条样本包含 DNA 序列、区间染色体/start/end 元数据、目标张量和 mask；dtype 与 resolution 见 `metadata/schema.yaml`。
|
| 35 |
+
|
| 36 |
+
## 数据集使用方式
|
| 37 |
+
|
| 38 |
+
### 文件与下载
|
| 39 |
+
|
| 40 |
+
独立下载：
|
| 41 |
+
|
| 42 |
+
```bash
|
| 43 |
+
hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir .
|
| 44 |
+
```
|
| 45 |
+
|
| 46 |
+
在模型包内使用：
|
| 47 |
+
|
| 48 |
+
```bash
|
| 49 |
+
hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir data/alphagenome_dataset
|
| 50 |
+
```
|
| 51 |
+
|
| 52 |
+
### 数据放置与验证
|
| 53 |
+
|
| 54 |
+
作为模型依赖使用时，推荐目录结构：
|
| 55 |
+
|
| 56 |
+
```text
|
| 57 |
+
<model-package>/data/alphagenome_dataset/
|
| 58 |
+
├── manifest.yaml
|
| 59 |
+
├── metadata/
|
| 60 |
+
├── reference/
|
| 61 |
+
└── v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 62 |
+
```
|
| 63 |
+
|
| 64 |
+
快速验证文件存在、大小和 gzip 可读性：
|
| 65 |
+
|
| 66 |
+
```bash
|
| 67 |
+
python scripts/validate_dataset.py --root .
|
| 68 |
+
```
|
| 69 |
+
|
| 70 |
+
全量 SHA256 验证可加 `--check-sha256`。
|
| 71 |
+
|
| 72 |
+
## OneScience 官方信息
|
| 73 |
+
|
| 74 |
+
| 平台 | OneScience 主仓库 | Skills 仓库 |
|
| 75 |
+
|---|---|---|
|
| 76 |
+
| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
|
| 77 |
+
| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |
|
| 78 |
+
|
| 79 |
+
## 限制与许可证
|
| 80 |
+
|
| 81 |
+
license: mixed
|
| 82 |
+
license_note: >
|
| 83 |
+
AlphaGenome training, validation and test datasets contain reprocessed
|
| 84 |
+
data from FANTOM5, 4D Nucleome, ENCODE and GENCODE. Usage is subject
|
| 85 |
+
to the respective source-specific licenses and data-use policies.
|
| 86 |
+
Other unspecified materials are licensed under CC BY-NC 4.0.
|
fasttrans-client.tar.gz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:ef4592c4701073b96e166f533364cb049be7e1ebbd093254fcac4ce4847140f2
|
| 3 |
+
size 30145032
|
fasttrans/install_rayfile.sh
ADDED
|
@@ -0,0 +1,14 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/bash
|
| 2 |
+
|
| 3 |
+
if ! type rayfile-c >/dev/null 2>&1; then
|
| 4 |
+
raytar="rayfile-c"
|
| 5 |
+
folder="/usr/local/rayfile"
|
| 6 |
+
if [ ! -d ${folder} ]; then
|
| 7 |
+
mkdir ${folder}
|
| 8 |
+
fi
|
| 9 |
+
cp -f ${raytar} ${folder} > /dev/null 2>&1
|
| 10 |
+
cp -f ${raytar} /usr/local/bin > /dev/null 2>&1
|
| 11 |
+
echo "Rayfile client installed successfully!"
|
| 12 |
+
else
|
| 13 |
+
echo "Rayfile client already installed! You can try 'rayfile-c'"
|
| 14 |
+
fi
|
fasttrans/rayfile-c
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:f718db7def476df9cdb259e0424b54bb0d0f82ed864adb84c62730b73d01b0a7
|
| 3 |
+
size 111146248
|
fasttrans/readme.txt
ADDED
|
@@ -0,0 +1,5 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
1、请上传安装包fasttrans-client.tar.gz到linux服务器
|
| 2 |
+
2、解压安装包：tar -zxf fasttrans-client.tar.gz
|
| 3 |
+
3、复制快传命令在linux服务器执行（注：fasttrans目录内执行需要在命令前增加“./”，如./rayfile-c）
|
| 4 |
+
4、如果想在任意目录执行rayfile-c，需要root权限用户执行install_rayfile.sh
|
| 5 |
+
|
manifest.yaml
ADDED
|
@@ -0,0 +1,291 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
onescience_manifest_version: "0.1"
|
| 2 |
+
resource_type: dataset
|
| 3 |
+
resource:
|
| 4 |
+
id: OneScience/alphagenome_dataset
|
| 5 |
+
name: AlphaGenome Dataset
|
| 6 |
+
domain: bio
|
| 7 |
+
domain_tags: [bio, genomics, regulatory_genomics]
|
| 8 |
+
task: regulatory_genomics_training_and_evaluation
|
| 9 |
+
task_tags: [reference_genome, tfrecord, evaluation, training]
|
| 10 |
+
modalities: [dna_sequence, functional_genomics_tracks, variants]
|
| 11 |
+
input_formats: [fasta, fai, feather, tfrecord]
|
| 12 |
+
output_formats: []
|
| 13 |
+
summary: AlphaGenome 参考基因组、注释文件和 HOMO_SAPIENS VALID TFRecord 数据，可供 OneScience AlphaGenome 预检、推理、变异评分和评测使用。
|
| 14 |
+
|
| 15 |
+
platform_resource:
|
| 16 |
+
primary:
|
| 17 |
+
platform: modelscope
|
| 18 |
+
repo_id: OneScience/alphagenome_dataset
|
| 19 |
+
repo_type: dataset
|
| 20 |
+
url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset
|
| 21 |
+
revision: main
|
| 22 |
+
readme_path: README.md
|
| 23 |
+
manifest_path: manifest.yaml
|
| 24 |
+
mirrors: []
|
| 25 |
+
access:
|
| 26 |
+
visibility: public
|
| 27 |
+
license: alphagenome-dataset-terms
|
| 28 |
+
|
| 29 |
+
website_integration:
|
| 30 |
+
enabled: true
|
| 31 |
+
click_target:
|
| 32 |
+
platform: modelscope
|
| 33 |
+
resource_url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset
|
| 34 |
+
llm_handoff:
|
| 35 |
+
readme_required: true
|
| 36 |
+
manifest_required: true
|
| 37 |
+
download_readme_first: true
|
| 38 |
+
resolve_related_models: true
|
| 39 |
+
default_run_goal: dataset_validation
|
| 40 |
+
|
| 41 |
+
runtime:
|
| 42 |
+
enabled: true
|
| 43 |
+
onescience_domain: bio
|
| 44 |
+
min_onescience_version: null
|
| 45 |
+
supported_execution: [local, local_slurm, remote_slurm, scnet_mcp]
|
| 46 |
+
|
| 47 |
+
onescience:
|
| 48 |
+
repo: https://gitee.com/onescience-ai/onescience
|
| 49 |
+
official_links:
|
| 50 |
+
gitee:
|
| 51 |
+
doc: https://gitee.com/onescience-ai/onescience-doc
|
| 52 |
+
onescience: https://gitee.com/onescience-ai/onescience
|
| 53 |
+
skills: https://gitee.com/onescience-ai/oneskills
|
| 54 |
+
github:
|
| 55 |
+
doc: https://github.com/onescience-ai/OneScience-doc
|
| 56 |
+
onescience: https://github.com/onescience-ai/OneScience
|
| 57 |
+
skills: https://github.com/onescience-ai/oneskills
|
| 58 |
+
install:
|
| 59 |
+
required_by_default: false
|
| 60 |
+
command: bash install.sh bio
|
| 61 |
+
source_paths:
|
| 62 |
+
- src/onescience/flax_models/alphagenome/io/dataset.py
|
| 63 |
+
compatibility:
|
| 64 |
+
examples_path: examples/biosciences/alphagenome
|
| 65 |
+
status: examples_compatible
|
| 66 |
+
|
| 67 |
+
runtime_package:
|
| 68 |
+
kind: standard_runtime_package
|
| 69 |
+
package_root: .
|
| 70 |
+
standard_layout:
|
| 71 |
+
workdir: .
|
| 72 |
+
config_dir: metadata
|
| 73 |
+
checkpoint_dir: null
|
| 74 |
+
data_dir: .
|
| 75 |
+
output_dir: validation_outputs
|
| 76 |
+
apply_policy:
|
| 77 |
+
mode: direct_use
|
| 78 |
+
target: session_data_dir
|
| 79 |
+
overwrite: true
|
| 80 |
+
protect_installed_onescience: true
|
| 81 |
+
entry_files:
|
| 82 |
+
- metadata/schema.yaml
|
| 83 |
+
- metadata/file_manifest.yaml
|
| 84 |
+
- scripts/validate_dataset.py
|
| 85 |
+
entrypoints:
|
| 86 |
+
preflight: scripts/validate_dataset.py
|
| 87 |
+
inference: null
|
| 88 |
+
train: null
|
| 89 |
+
finetune: null
|
| 90 |
+
evaluate: null
|
| 91 |
+
visualize: null
|
| 92 |
+
deploy: null
|
| 93 |
+
|
| 94 |
+
files:
|
| 95 |
+
dataset_files:
|
| 96 |
+
- id: file_manifest
|
| 97 |
+
path: metadata/file_manifest.yaml
|
| 98 |
+
role: integrity_manifest
|
| 99 |
+
format: yaml
|
| 100 |
+
description_zh: 逐文件记录原始文件名、大小和 SHA256，用于校验整理后数据与原始数据一致。
|
| 101 |
+
required: true
|
| 102 |
+
required_for: [preflight, train, evaluate, inference]
|
| 103 |
+
source:
|
| 104 |
+
platform: modelscope
|
| 105 |
+
repo_id: OneScience/alphagenome_dataset
|
| 106 |
+
repo_type: dataset
|
| 107 |
+
path: metadata/file_manifest.yaml
|
| 108 |
+
revision: main
|
| 109 |
+
download_method: command_ref
|
| 110 |
+
command_ref: commands.download.download_dataset
|
| 111 |
+
local_path: metadata/file_manifest.yaml
|
| 112 |
+
- id: schema
|
| 113 |
+
path: metadata/schema.yaml
|
| 114 |
+
role: schema
|
| 115 |
+
format: yaml
|
| 116 |
+
description_zh: 描述 TFRecord bundle、tensor dtype、参考基因组和可用 split。
|
| 117 |
+
required: true
|
| 118 |
+
required_for: [preflight, train, evaluate]
|
| 119 |
+
local_path: metadata/schema.yaml
|
| 120 |
+
- id: reference_genomes
|
| 121 |
+
path: reference/
|
| 122 |
+
role: reference_genome
|
| 123 |
+
format: fasta_fai_feather
|
| 124 |
+
description_zh: 人和小鼠参考基因组、FAI 索引、Gencode 和剪接/多聚腺苷酸化注释 feather 文件。
|
| 125 |
+
required: true
|
| 126 |
+
required_for: [preflight, inference, variant_scoring]
|
| 127 |
+
source:
|
| 128 |
+
platform: modelscope
|
| 129 |
+
repo_id: OneScience/alphagenome_dataset
|
| 130 |
+
repo_type: dataset
|
| 131 |
+
path: reference/
|
| 132 |
+
revision: main
|
| 133 |
+
download_method: command_ref
|
| 134 |
+
command_ref: commands.download.download_dataset
|
| 135 |
+
local_path: reference/
|
| 136 |
+
- id: valid_tfrecords
|
| 137 |
+
path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 138 |
+
role: evaluation_data
|
| 139 |
+
format: gzipped_tfrecord
|
| 140 |
+
description_zh: HOMO_SAPIENS ALL_FOLDS VALID split，12 个 bundle，每个 bundle 25 个 gzipped TFRecord 分片。
|
| 141 |
+
required: true
|
| 142 |
+
required_for: [preflight, evaluate]
|
| 143 |
+
source:
|
| 144 |
+
platform: modelscope
|
| 145 |
+
repo_id: OneScience/alphagenome_dataset
|
| 146 |
+
repo_type: dataset
|
| 147 |
+
path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 148 |
+
revision: main
|
| 149 |
+
download_method: command_ref
|
| 150 |
+
command_ref: commands.download.download_dataset
|
| 151 |
+
local_path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 152 |
+
- id: fasttrans_tools
|
| 153 |
+
path: fasttrans/
|
| 154 |
+
role: transfer_tool
|
| 155 |
+
format: binary
|
| 156 |
+
description_zh: 原始数据随附的 fasttrans 传输工具和说明，运行 AlphaGenome 不依赖该工具。
|
| 157 |
+
required: false
|
| 158 |
+
required_for: []
|
| 159 |
+
local_path: fasttrans/
|
| 160 |
+
config_files: []
|
| 161 |
+
sample_files: []
|
| 162 |
+
script_files:
|
| 163 |
+
- id: validate_dataset
|
| 164 |
+
path: scripts/validate_dataset.py
|
| 165 |
+
role: preflight
|
| 166 |
+
description_zh: 根据 metadata/file_manifest.yaml 校验文件名、大小、可选 SHA256 和 TFRecord gzip 可读性。
|
| 167 |
+
required: true
|
| 168 |
+
required_for: [preflight]
|
| 169 |
+
|
| 170 |
+
dataset:
|
| 171 |
+
format: [gzipped_tfrecord, fasta, fai, feather]
|
| 172 |
+
sample_unit: 一个 TFRecord example 包含 1,052,672 bp DNA 序列、区间元数据以及某个 bundle 的目标张量和 mask。
|
| 173 |
+
schema:
|
| 174 |
+
path: metadata/schema.yaml
|
| 175 |
+
integrity_manifest:
|
| 176 |
+
path: metadata/file_manifest.yaml
|
| 177 |
+
file_count: 315
|
| 178 |
+
includes_sha256: true
|
| 179 |
+
splits:
|
| 180 |
+
train: null
|
| 181 |
+
validation: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 182 |
+
test: null
|
| 183 |
+
|
| 184 |
+
relations:
|
| 185 |
+
required_datasets: []
|
| 186 |
+
optional_datasets: []
|
| 187 |
+
compatible_models:
|
| 188 |
+
- id: OneScience/alphagenome/
|
| 189 |
+
role: reference_and_eval_data
|
| 190 |
+
required_for: [preflight, inference, variant_scoring, evaluate]
|
| 191 |
+
resource_ref:
|
| 192 |
+
platform: modelscope
|
| 193 |
+
repo_id: OneScience/alphagenome/
|
| 194 |
+
repo_type: model
|
| 195 |
+
url: https://modelscope.cn/models/OneScience/alphagenome/
|
| 196 |
+
revision: main
|
| 197 |
+
readme_path: README.md
|
| 198 |
+
manifest_path: manifest.yaml
|
| 199 |
+
expected_local_path: data/alphagenome_dataset
|
| 200 |
+
adapter: null
|
| 201 |
+
|
| 202 |
+
run_matrix:
|
| 203 |
+
scenarios:
|
| 204 |
+
- name: dataset_validation
|
| 205 |
+
default: true
|
| 206 |
+
goal: minimal_validation
|
| 207 |
+
required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords]
|
| 208 |
+
required_model_files: []
|
| 209 |
+
required_datasets: []
|
| 210 |
+
command_refs: [commands.preflight.validate_dataset_fast]
|
| 211 |
+
outputs: [dataset_validation_stdout]
|
| 212 |
+
prerequisites:
|
| 213 |
+
- cwd 为数据集包根目录。
|
| 214 |
+
- name: dataset_validation_full_sha256
|
| 215 |
+
goal: integrity_validation
|
| 216 |
+
required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords]
|
| 217 |
+
required_model_files: []
|
| 218 |
+
required_datasets: []
|
| 219 |
+
command_refs: [commands.preflight.validate_dataset_full_sha256]
|
| 220 |
+
outputs: [dataset_validation_stdout]
|
| 221 |
+
prerequisites:
|
| 222 |
+
- cwd 为数据集包根目录。
|
| 223 |
+
- 允许读取全部 114G 数据计算 SHA256。
|
| 224 |
+
|
| 225 |
+
capabilities:
|
| 226 |
+
inference: false
|
| 227 |
+
train: true
|
| 228 |
+
finetune: true
|
| 229 |
+
evaluate: true
|
| 230 |
+
visualize: false
|
| 231 |
+
deploy: false
|
| 232 |
+
|
| 233 |
+
commands:
|
| 234 |
+
download:
|
| 235 |
+
- name: download_dataset
|
| 236 |
+
cwd: .
|
| 237 |
+
command: modelscope download --dataset OneScience/alphagenome_dataset --local_dir .
|
| 238 |
+
description_zh: 下载 AlphaGenome 数据集包到当前目录。
|
| 239 |
+
preflight:
|
| 240 |
+
- name: validate_dataset_fast
|
| 241 |
+
cwd: .
|
| 242 |
+
command: python scripts/validate_dataset.py --root .
|
| 243 |
+
description_zh: 快速校验文件存在、大小一致并抽查 TFRecord gzip 可读性。
|
| 244 |
+
- name: validate_dataset_full_sha256
|
| 245 |
+
cwd: .
|
| 246 |
+
command: python scripts/validate_dataset.py --root . --check-sha256
|
| 247 |
+
description_zh: 全量校验文件名、大小和 SHA256，耗时取决于存储带宽。
|
| 248 |
+
prepare: []
|
| 249 |
+
inference: []
|
| 250 |
+
train: []
|
| 251 |
+
finetune: []
|
| 252 |
+
evaluate: []
|
| 253 |
+
visualize: []
|
| 254 |
+
deploy: []
|
| 255 |
+
|
| 256 |
+
expected_outputs:
|
| 257 |
+
- id: dataset_validation_stdout
|
| 258 |
+
path: stdout
|
| 259 |
+
description_zh: "输出 dataset_validation_ok: true、checked_files 和 total_size_bytes。"
|
| 260 |
+
|
| 261 |
+
diagnostics:
|
| 262 |
+
- id: missing_file
|
| 263 |
+
match: "missing file"
|
| 264 |
+
severity: error
|
| 265 |
+
message_zh: 数据文件缺失。
|
| 266 |
+
fix_zh: 重新执行 modelscope download --dataset OneScience/alphagenome_dataset，并确认下载位置为数据集包根目录。
|
| 267 |
+
- id: size_mismatch
|
| 268 |
+
match: "size mismatch"
|
| 269 |
+
severity: error
|
| 270 |
+
message_zh: 整理后文件大小与原始清单不一致。
|
| 271 |
+
fix_zh: 删除损坏文件后重新下载，或从原始路径重新实体复制；用于上传的目录不能使用软链接代替真实文件。
|
| 272 |
+
- id: sha256_mismatch
|
| 273 |
+
match: "sha256 mismatch"
|
| 274 |
+
severity: error
|
| 275 |
+
message_zh: 文件内容与原始清单不一致。
|
| 276 |
+
fix_zh: 重新下载对应文件并再次执行全量 SHA256 校验。
|
| 277 |
+
- id: gzip_unreadable
|
| 278 |
+
match: "gzip TFRecord is unreadable"
|
| 279 |
+
severity: error
|
| 280 |
+
message_zh: TFRecord gzip 压缩流无法读取。
|
| 281 |
+
fix_zh: 重新下载对应 TFRecord 分片。
|
| 282 |
+
|
| 283 |
+
domain_extension:
|
| 284 |
+
bio:
|
| 285 |
+
organisms: [HOMO_SAPIENS, MUS_MUSCULUS]
|
| 286 |
+
genome_builds:
|
| 287 |
+
HOMO_SAPIENS: GRCh38.p13
|
| 288 |
+
MUS_MUSCULUS: GRCm38.p6
|
| 289 |
+
available_split: ALL_FOLDS/HOMO_SAPIENS/VALID
|
| 290 |
+
bundle_count: 12
|
| 291 |
+
shards_per_bundle: 25
|
metadata/file_manifest.yaml
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
metadata/schema.yaml
ADDED
|
@@ -0,0 +1,71 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
dataset: AlphaGenome
|
| 2 |
+
repo_id: OneScience/alphagenome_dataset
|
| 3 |
+
format:
|
| 4 |
+
- gzipped TFRecord
|
| 5 |
+
- FASTA
|
| 6 |
+
- FASTA index
|
| 7 |
+
- feather
|
| 8 |
+
organisms:
|
| 9 |
+
- HOMO_SAPIENS
|
| 10 |
+
- MUS_MUSCULUS
|
| 11 |
+
splits:
|
| 12 |
+
available:
|
| 13 |
+
- ALL_FOLDS/HOMO_SAPIENS/VALID
|
| 14 |
+
bundles:
|
| 15 |
+
ATAC:
|
| 16 |
+
tensors:
|
| 17 |
+
atac: bfloat16
|
| 18 |
+
atac_mask: bool
|
| 19 |
+
resolution_bp: 1
|
| 20 |
+
DNASE:
|
| 21 |
+
tensors:
|
| 22 |
+
dnase: bfloat16
|
| 23 |
+
dnase_mask: bool
|
| 24 |
+
resolution_bp: 1
|
| 25 |
+
CAGE:
|
| 26 |
+
tensors:
|
| 27 |
+
cage: bfloat16
|
| 28 |
+
cage_mask: bool
|
| 29 |
+
resolution_bp: 1
|
| 30 |
+
RNA_SEQ:
|
| 31 |
+
tensors:
|
| 32 |
+
rna_seq: bfloat16
|
| 33 |
+
rna_seq_mask: bool
|
| 34 |
+
rna_seq_strand: int32
|
| 35 |
+
resolution_bp: 1
|
| 36 |
+
CHIP_TF:
|
| 37 |
+
tensors:
|
| 38 |
+
chip_tf: float32
|
| 39 |
+
chip_tf_mask: bool
|
| 40 |
+
resolution_bp: 128
|
| 41 |
+
CHIP_HISTONE:
|
| 42 |
+
tensors:
|
| 43 |
+
chip_histone: float32
|
| 44 |
+
chip_histone_mask: bool
|
| 45 |
+
resolution_bp: 128
|
| 46 |
+
CONTACT_MAPS:
|
| 47 |
+
tensors:
|
| 48 |
+
contact_maps: float32
|
| 49 |
+
resolution_bp: 2048
|
| 50 |
+
PROCAP:
|
| 51 |
+
tensors:
|
| 52 |
+
procap: bfloat16
|
| 53 |
+
procap_mask: bool
|
| 54 |
+
resolution_bp: 1
|
| 55 |
+
SPLICE_SITES:
|
| 56 |
+
tensors:
|
| 57 |
+
splice_sites: bool
|
| 58 |
+
resolution_bp: 1
|
| 59 |
+
SPLICE_SITE_USAGE:
|
| 60 |
+
tensors:
|
| 61 |
+
splice_site_usage: float16
|
| 62 |
+
resolution_bp: 1
|
| 63 |
+
SPLICE_JUNCTIONS:
|
| 64 |
+
tensors:
|
| 65 |
+
splice_junctions: float32
|
| 66 |
+
resolution_bp: 1
|
| 67 |
+
SPLICE_SITE_POSITIONS:
|
| 68 |
+
tensors:
|
| 69 |
+
splice_site_positions: int32
|
| 70 |
+
resolution_bp: 1
|
| 71 |
+
sample_unit: 一个 TFRecord example 包含 1,052,672 bp DNA 序列、区间元数据以及某个 bundle 的目标张量和 mask。
|
onescience_run_manifest.yaml
ADDED
|
@@ -0,0 +1,291 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
| 1 |
+
onescience_manifest_version: "0.1"
|
| 2 |
+
resource_type: dataset
|
| 3 |
+
resource:
|
| 4 |
+
id: OneScience/alphagenome_dataset
|
| 5 |
+
name: AlphaGenome Dataset
|
| 6 |
+
domain: bio
|
| 7 |
+
domain_tags: [bio, genomics, regulatory_genomics]
|
| 8 |
+
task: regulatory_genomics_training_and_evaluation
|
| 9 |
+
task_tags: [reference_genome, tfrecord, evaluation, training]
|
| 10 |
+
modalities: [dna_sequence, functional_genomics_tracks, variants]
|
| 11 |
+
input_formats: [fasta, fai, feather, tfrecord]
|
| 12 |
+
output_formats: []
|
| 13 |
+
summary: AlphaGenome 参考基因组、注释文件和 HOMO_SAPIENS VALID TFRecord 数据，可供 OneScience AlphaGenome 预检、推理、变异评分和评测使用。
|
| 14 |
+
|
| 15 |
+
platform_resource:
|
| 16 |
+
primary:
|
| 17 |
+
platform: modelscope
|
| 18 |
+
repo_id: OneScience/alphagenome_dataset
|
| 19 |
+
repo_type: dataset
|
| 20 |
+
url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset
|
| 21 |
+
revision: main
|
| 22 |
+
readme_path: README.md
|
| 23 |
+
manifest_path: manifest.yaml
|
| 24 |
+
mirrors: []
|
| 25 |
+
access:
|
| 26 |
+
visibility: public
|
| 27 |
+
license: alphagenome-dataset-terms
|
| 28 |
+
|
| 29 |
+
website_integration:
|
| 30 |
+
enabled: true
|
| 31 |
+
click_target:
|
| 32 |
+
platform: modelscope
|
| 33 |
+
resource_url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset
|
| 34 |
+
llm_handoff:
|
| 35 |
+
readme_required: true
|
| 36 |
+
manifest_required: true
|
| 37 |
+
download_readme_first: true
|
| 38 |
+
resolve_related_models: true
|
| 39 |
+
default_run_goal: dataset_validation
|
| 40 |
+
|
| 41 |
+
runtime:
|
| 42 |
+
enabled: true
|
| 43 |
+
onescience_domain: bio
|
| 44 |
+
min_onescience_version: null
|
| 45 |
+
supported_execution: [local, local_slurm, remote_slurm, scnet_mcp]
|
| 46 |
+
|
| 47 |
+
onescience:
|
| 48 |
+
repo: https://gitee.com/onescience-ai/onescience
|
| 49 |
+
official_links:
|
| 50 |
+
gitee:
|
| 51 |
+
doc: https://gitee.com/onescience-ai/onescience-doc
|
| 52 |
+
onescience: https://gitee.com/onescience-ai/onescience
|
| 53 |
+
skills: https://gitee.com/onescience-ai/oneskills
|
| 54 |
+
github:
|
| 55 |
+
doc: https://github.com/onescience-ai/OneScience-doc
|
| 56 |
+
onescience: https://github.com/onescience-ai/OneScience
|
| 57 |
+
skills: https://github.com/onescience-ai/oneskills
|
| 58 |
+
install:
|
| 59 |
+
required_by_default: false
|
| 60 |
+
command: bash install.sh bio
|
| 61 |
+
source_paths:
|
| 62 |
+
- src/onescience/flax_models/alphagenome/io/dataset.py
|
| 63 |
+
compatibility:
|
| 64 |
+
examples_path: examples/biosciences/alphagenome
|
| 65 |
+
status: examples_compatible
|
| 66 |
+
|
| 67 |
+
runtime_package:
|
| 68 |
+
kind: standard_runtime_package
|
| 69 |
+
package_root: .
|
| 70 |
+
standard_layout:
|
| 71 |
+
workdir: .
|
| 72 |
+
config_dir: metadata
|
| 73 |
+
checkpoint_dir: null
|
| 74 |
+
data_dir: .
|
| 75 |
+
output_dir: validation_outputs
|
| 76 |
+
apply_policy:
|
| 77 |
+
mode: direct_use
|
| 78 |
+
target: session_data_dir
|
| 79 |
+
overwrite: true
|
| 80 |
+
protect_installed_onescience: true
|
| 81 |
+
entry_files:
|
| 82 |
+
- metadata/schema.yaml
|
| 83 |
+
- metadata/file_manifest.yaml
|
| 84 |
+
- scripts/validate_dataset.py
|
| 85 |
+
entrypoints:
|
| 86 |
+
preflight: scripts/validate_dataset.py
|
| 87 |
+
inference: null
|
| 88 |
+
train: null
|
| 89 |
+
finetune: null
|
| 90 |
+
evaluate: null
|
| 91 |
+
visualize: null
|
| 92 |
+
deploy: null
|
| 93 |
+
|
| 94 |
+
files:
|
| 95 |
+
dataset_files:
|
| 96 |
+
- id: file_manifest
|
| 97 |
+
path: metadata/file_manifest.yaml
|
| 98 |
+
role: integrity_manifest
|
| 99 |
+
format: yaml
|
| 100 |
+
description_zh: 逐文件记录原始文件名、大小和 SHA256，用于校验整理后数据与原始数据一致。
|
| 101 |
+
required: true
|
| 102 |
+
required_for: [preflight, train, evaluate, inference]
|
| 103 |
+
source:
|
| 104 |
+
platform: modelscope
|
| 105 |
+
repo_id: OneScience/alphagenome_dataset
|
| 106 |
+
repo_type: dataset
|
| 107 |
+
path: metadata/file_manifest.yaml
|
| 108 |
+
revision: main
|
| 109 |
+
download_method: command_ref
|
| 110 |
+
command_ref: commands.download.download_dataset
|
| 111 |
+
local_path: metadata/file_manifest.yaml
|
| 112 |
+
- id: schema
|
| 113 |
+
path: metadata/schema.yaml
|
| 114 |
+
role: schema
|
| 115 |
+
format: yaml
|
| 116 |
+
description_zh: 描述 TFRecord bundle、tensor dtype、参考基因组和可用 split。
|
| 117 |
+
required: true
|
| 118 |
+
required_for: [preflight, train, evaluate]
|
| 119 |
+
local_path: metadata/schema.yaml
|
| 120 |
+
- id: reference_genomes
|
| 121 |
+
path: reference/
|
| 122 |
+
role: reference_genome
|
| 123 |
+
format: fasta_fai_feather
|
| 124 |
+
description_zh: 人和小鼠参考基因组、FAI 索引、Gencode 和剪接/多聚腺苷酸化注释 feather 文件。
|
| 125 |
+
required: true
|
| 126 |
+
required_for: [preflight, inference, variant_scoring]
|
| 127 |
+
source:
|
| 128 |
+
platform: modelscope
|
| 129 |
+
repo_id: OneScience/alphagenome_dataset
|
| 130 |
+
repo_type: dataset
|
| 131 |
+
path: reference/
|
| 132 |
+
revision: main
|
| 133 |
+
download_method: command_ref
|
| 134 |
+
command_ref: commands.download.download_dataset
|
| 135 |
+
local_path: reference/
|
| 136 |
+
- id: valid_tfrecords
|
| 137 |
+
path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 138 |
+
role: evaluation_data
|
| 139 |
+
format: gzipped_tfrecord
|
| 140 |
+
description_zh: HOMO_SAPIENS ALL_FOLDS VALID split，12 个 bundle，每个 bundle 25 个 gzipped TFRecord 分片。
|
| 141 |
+
required: true
|
| 142 |
+
required_for: [preflight, evaluate]
|
| 143 |
+
source:
|
| 144 |
+
platform: modelscope
|
| 145 |
+
repo_id: OneScience/alphagenome_dataset
|
| 146 |
+
repo_type: dataset
|
| 147 |
+
path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 148 |
+
revision: main
|
| 149 |
+
download_method: command_ref
|
| 150 |
+
command_ref: commands.download.download_dataset
|
| 151 |
+
local_path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 152 |
+
- id: fasttrans_tools
|
| 153 |
+
path: fasttrans/
|
| 154 |
+
role: transfer_tool
|
| 155 |
+
format: binary
|
| 156 |
+
description_zh: 原始数据随附的 fasttrans 传输工具和说明，运行 AlphaGenome 不依赖该工具。
|
| 157 |
+
required: false
|
| 158 |
+
required_for: []
|
| 159 |
+
local_path: fasttrans/
|
| 160 |
+
config_files: []
|
| 161 |
+
sample_files: []
|
| 162 |
+
script_files:
|
| 163 |
+
- id: validate_dataset
|
| 164 |
+
path: scripts/validate_dataset.py
|
| 165 |
+
role: preflight
|
| 166 |
+
description_zh: 根据 metadata/file_manifest.yaml 校验文件名、大小、可选 SHA256 和 TFRecord gzip 可读性。
|
| 167 |
+
required: true
|
| 168 |
+
required_for: [preflight]
|
| 169 |
+
|
| 170 |
+
dataset:
|
| 171 |
+
format: [gzipped_tfrecord, fasta, fai, feather]
|
| 172 |
+
sample_unit: 一个 TFRecord example 包含 1,052,672 bp DNA 序列、区间元数据以及某个 bundle 的目标张量和 mask。
|
| 173 |
+
schema:
|
| 174 |
+
path: metadata/schema.yaml
|
| 175 |
+
integrity_manifest:
|
| 176 |
+
path: metadata/file_manifest.yaml
|
| 177 |
+
file_count: 315
|
| 178 |
+
includes_sha256: true
|
| 179 |
+
splits:
|
| 180 |
+
train: null
|
| 181 |
+
validation: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/
|
| 182 |
+
test: null
|
| 183 |
+
|
| 184 |
+
relations:
|
| 185 |
+
required_datasets: []
|
| 186 |
+
optional_datasets: []
|
| 187 |
+
compatible_models:
|
| 188 |
+
- id: OneScience/alphagenome/
|
| 189 |
+
role: reference_and_eval_data
|
| 190 |
+
required_for: [preflight, inference, variant_scoring, evaluate]
|
| 191 |
+
resource_ref:
|
| 192 |
+
platform: modelscope
|
| 193 |
+
repo_id: OneScience/alphagenome/
|
| 194 |
+
repo_type: model
|
| 195 |
+
url: https://modelscope.cn/models/OneScience/alphagenome/
|
| 196 |
+
revision: main
|
| 197 |
+
readme_path: README.md
|
| 198 |
+
manifest_path: manifest.yaml
|
| 199 |
+
expected_local_path: data/alphagenome_dataset
|
| 200 |
+
adapter: null
|
| 201 |
+
|
| 202 |
+
run_matrix:
|
| 203 |
+
scenarios:
|
| 204 |
+
- name: dataset_validation
|
| 205 |
+
default: true
|
| 206 |
+
goal: minimal_validation
|
| 207 |
+
required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords]
|
| 208 |
+
required_model_files: []
|
| 209 |
+
required_datasets: []
|
| 210 |
+
command_refs: [commands.preflight.validate_dataset_fast]
|
| 211 |
+
outputs: [dataset_validation_stdout]
|
| 212 |
+
prerequisites:
|
| 213 |
+
- cwd 为数据集包根目录。
|
| 214 |
+
- name: dataset_validation_full_sha256
|
| 215 |
+
goal: integrity_validation
|
| 216 |
+
required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords]
|
| 217 |
+
required_model_files: []
|
| 218 |
+
required_datasets: []
|
| 219 |
+
command_refs: [commands.preflight.validate_dataset_full_sha256]
|
| 220 |
+
outputs: [dataset_validation_stdout]
|
| 221 |
+
prerequisites:
|
| 222 |
+
- cwd 为数据集包根目录。
|
| 223 |
+
- 允许读取全部 114G 数据计算 SHA256。
|
| 224 |
+
|
| 225 |
+
capabilities:
|
| 226 |
+
inference: false
|
| 227 |
+
train: true
|
| 228 |
+
finetune: true
|
| 229 |
+
evaluate: true
|
| 230 |
+
visualize: false
|
| 231 |
+
deploy: false
|
| 232 |
+
|
| 233 |
+
commands:
|
| 234 |
+
download:
|
| 235 |
+
- name: download_dataset
|
| 236 |
+
cwd: .
|
| 237 |
+
command: modelscope download --dataset OneScience/alphagenome_dataset --local_dir .
|
| 238 |
+
description_zh: 下载 AlphaGenome 数据集包到当前目录。
|
| 239 |
+
preflight:
|
| 240 |
+
- name: validate_dataset_fast
|
| 241 |
+
cwd: .
|
| 242 |
+
command: python scripts/validate_dataset.py --root .
|
| 243 |
+
description_zh: 快速校验文件存在、大小一致并抽查 TFRecord gzip 可读性。
|
| 244 |
+
- name: validate_dataset_full_sha256
|
| 245 |
+
cwd: .
|
| 246 |
+
command: python scripts/validate_dataset.py --root . --check-sha256
|
| 247 |
+
description_zh: 全量校验文件名、大小和 SHA256，耗时取决于存储带宽。
|
| 248 |
+
prepare: []
|
| 249 |
+
inference: []
|
| 250 |
+
train: []
|
| 251 |
+
finetune: []
|
| 252 |
+
evaluate: []
|
| 253 |
+
visualize: []
|
| 254 |
+
deploy: []
|
| 255 |
+
|
| 256 |
+
expected_outputs:
|
| 257 |
+
- id: dataset_validation_stdout
|
| 258 |
+
path: stdout
|
| 259 |
+
description_zh: "输出 dataset_validation_ok: true、checked_files 和 total_size_bytes。"
|
| 260 |
+
|
| 261 |
+
diagnostics:
|
| 262 |
+
- id: missing_file
|
| 263 |
+
match: "missing file"
|
| 264 |
+
severity: error
|
| 265 |
+
message_zh: 数据文件缺失。
|
| 266 |
+
fix_zh: 重新执行 modelscope download --dataset OneScience/alphagenome_dataset，并确认下载位置为数据集包根目录。
|
| 267 |
+
- id: size_mismatch
|
| 268 |
+
match: "size mismatch"
|
| 269 |
+
severity: error
|
| 270 |
+
message_zh: 整理后文件大小与原始清单不一致。
|
| 271 |
+
fix_zh: 删除损坏文件后重新下载，或从原始路径重新实体复制；用于上传的目录不能使用软链接代替真实文件。
|
| 272 |
+
- id: sha256_mismatch
|
| 273 |
+
match: "sha256 mismatch"
|
| 274 |
+
severity: error
|
| 275 |
+
message_zh: 文件内容与原始清单不一致。
|
| 276 |
+
fix_zh: 重新下载对应文件并再次执行全量 SHA256 校验。
|
| 277 |
+
- id: gzip_unreadable
|
| 278 |
+
match: "gzip TFRecord is unreadable"
|
| 279 |
+
severity: error
|
| 280 |
+
message_zh: TFRecord gzip 压缩流无法读取。
|
| 281 |
+
fix_zh: 重新下载对应 TFRecord 分片。
|
| 282 |
+
|
| 283 |
+
domain_extension:
|
| 284 |
+
bio:
|
| 285 |
+
organisms: [HOMO_SAPIENS, MUS_MUSCULUS]
|
| 286 |
+
genome_builds:
|
| 287 |
+
HOMO_SAPIENS: GRCh38.p13
|
| 288 |
+
MUS_MUSCULUS: GRCm38.p6
|
| 289 |
+
available_split: ALL_FOLDS/HOMO_SAPIENS/VALID
|
| 290 |
+
bundle_count: 12
|
| 291 |
+
shards_per_bundle: 25
|
reference/HOMO_SAPIENS/GRCh38.p13.genome.fa
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:28644d6230212c9daabf27ec17fb2a0928757ba6cfe4037b663ac22bd9063ed2
|
| 3 |
+
size 3321586957
|
reference/HOMO_SAPIENS/GRCh38.p13.genome.fa.fai
ADDED
|
@@ -0,0 +1,639 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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| 1 |
+
chr1 248956422 8 60 61
|
| 2 |
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chr2 242193529 253105712 60 61
|
| 3 |
+
chr3 198295559 499335808 60 61
|
| 4 |
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chr4 190214555 700936301 60 61
|
| 5 |
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chr5 181538259 894321107 60 61
|
| 6 |
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chr6 170805979 1078885012 60 61
|
| 7 |
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chr7 159345973 1252537766 60 61
|
| 8 |
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chr8 145138636 1414539514 60 61
|
| 9 |
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chr9 138394717 1562097136 60 61
|
| 10 |
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chr10 133797422 1702798442 60 61
|
| 11 |
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chr11 135086622 1838825832 60 61
|
| 12 |
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chr12 133275309 1976163908 60 61
|
| 13 |
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chr13 114364328 2111660483 60 61
|
| 14 |
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chr14 107043718 2227930894 60 61
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| 15 |
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chr15 101991189 2336758684 60 61
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| 16 |
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chr16 90338345 2440449737 60 61
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| 17 |
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chr17 83257441 2532293732 60 61
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| 18 |
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chr18 80373285 2616938808 60 61
|
| 19 |
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chr19 58617616 2698651658 60 61
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| 20 |
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chr20 64444167 2758246245 60 61
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| 21 |
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chr21 46709983 2823764492 60 61
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| 22 |
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chr22 50818468 2871252985 60 61
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| 23 |
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chrX 156040895 2922918436 60 61
|
| 24 |
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chrY 57227415 3081560021 60 61
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| 25 |
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chrM 16569 3139741236 60 61
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GL000008.2 209709 3139758105 60 61
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
chr1 195471971 8 60 61
|
| 2 |
+
chr2 182113224 198729854 60 61
|
| 3 |
+
chr3 160039680 383878307 60 61
|
| 4 |
+
chr4 156508116 546585323 60 61
|
| 5 |
+
chr5 151834684 705701916 60 61
|
| 6 |
+
chr6 149736546 860067187 60 61
|
| 7 |
+
chr7 145441459 1012299351 60 61
|
| 8 |
+
chr8 129401213 1160164843 60 61
|
| 9 |
+
chr9 124595110 1291722751 60 61
|
| 10 |
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chr10 130694993 1418394457 60 61
|
| 11 |
+
chr11 122082543 1551267710 60 61
|
| 12 |
+
chr12 120129022 1675384973 60 61
|
| 13 |
+
chr13 120421639 1797516156 60 61
|
| 14 |
+
chr14 124902244 1919944833 60 61
|
| 15 |
+
chr15 104043685 2046928792 60 61
|
| 16 |
+
chr16 98207768 2152706549 60 61
|
| 17 |
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chr17 94987271 2252551124 60 61
|
| 18 |
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chr18 90702639 2349121527 60 61
|
| 19 |
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chr19 61431566 2441335887 60 61
|
| 20 |
+
chrX 171031299 2503791321 60 61
|
| 21 |
+
chrY 91744698 2677673150 60 61
|
| 22 |
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chrM 16299 2770946936 60 61
|
| 23 |
+
KZ289080.1 394982 2770963540 60 61
|
| 24 |
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KZ289081.1 369973 2771365139 60 61
|
| 25 |
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GL456210.1 169725 2771741302 60 61
|
| 26 |
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GL456211.1 241735 2771913879 60 61
|
| 27 |
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GL456212.1 153618 2772159666 60 61
|
| 28 |
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GL456213.1 39340 2772315868 60 61
|
| 29 |
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GL456216.1 66673 2772355887 60 61
|
| 30 |
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GL456219.1 175968 2772423695 60 61
|
| 31 |
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GL456221.1 206961 2772602619 60 61
|
| 32 |
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GL456233.1 336933 2772813053 60 61
|
| 33 |
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GL456239.1 40056 2773155625 60 61
|
| 34 |
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GL456350.1 227966 2773196372 60 61
|
| 35 |
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GL456354.1 195993 2773428161 60 61
|
| 36 |
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GL456359.1 22974 2773627444 60 61
|
| 37 |
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GL456360.1 31704 2773650824 60 61
|
| 38 |
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GL456366.1 47073 2773683080 60 61
|
| 39 |
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GL456367.1 42057 2773730961 60 61
|
| 40 |
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GL456368.1 20208 2773773742 60 61
|
| 41 |
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GL456370.1 26764 2773794310 60 61
|
| 42 |
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GL456372.1 28664 2773821544 60 61
|
| 43 |
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GL456378.1 31602 2773850709 60 61
|
| 44 |
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GL456379.1 72385 2773882861 60 61
|
| 45 |
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GL456381.1 25871 2773956476 60 61
|
| 46 |
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GL456382.1 23158 2773982802 60 61
|
| 47 |
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GL456383.1 38659 2774006369 60 61
|
| 48 |
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GL456385.1 35240 2774045696 60 61
|
| 49 |
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GL456387.1 24685 2774081547 60 61
|
| 50 |
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GL456389.1 28772 2774106667 60 61
|
| 51 |
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GL456390.1 24668 2774135942 60 61
|
| 52 |
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GL456392.1 23629 2774161045 60 61
|
| 53 |
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GL456393.1 55711 2774185091 60 61
|
| 54 |
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GL456394.1 24323 2774241754 60 61
|
| 55 |
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GL456396.1 21240 2774266506 60 61
|
| 56 |
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JH584292.1 14945 2774288123 60 61
|
| 57 |
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|
| 58 |
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JH584294.1 191905 2774514799 60 61
|
| 59 |
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JH584295.1 1976 2774709926 60 61
|
| 60 |
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JH584296.1 199368 2774711958 60 61
|
| 61 |
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JH584297.1 205776 2774914672 60 61
|
| 62 |
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JH584298.1 184189 2775123901 60 61
|
| 63 |
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JH584299.1 953012 2775311183 60 61
|
| 64 |
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JH584300.1 182347 2776280102 60 61
|
| 65 |
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JH584301.1 259875 2776465512 60 61
|
| 66 |
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JH584302.1 155838 2776729742 60 61
|
| 67 |
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JH584303.1 158099 2776888201 60 61
|
| 68 |
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JH584304.1 114452 2777048958 60 61
|
| 69 |
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KZ289092.1 460895 2777165342 60 61
|
| 70 |
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KQ030490.1 120154 2777633943 60 61
|
| 71 |
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KB469738.3 210641 2777756124 60 61
|
| 72 |
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JH792830.1 246751 2777970300 60 61
|
| 73 |
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KV575237.1 1224174 2778221188 60 61
|
| 74 |
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KK082442.1 154766 2779465789 60 61
|
| 75 |
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KV575240.1 171859 2779623166 60 61
|
| 76 |
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KV575235.1 195735 2779797914 60 61
|
| 77 |
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KZ289088.1 328684 2779996936 60 61
|
| 78 |
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KV575239.1 71460 2780331124 60 61
|
| 79 |
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KQ030495.1 490000 2780403800 60 61
|
| 80 |
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KV575238.1 414410 2780901992 60 61
|
| 81 |
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KZ289082.1 111720 2781323334 60 61
|
| 82 |
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KV575234.1 686942 2781436941 60 61
|
| 83 |
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KZ289072.1 425386 2782135358 60 61
|
| 84 |
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KQ030485.1 185548 2782567859 60 61
|
| 85 |
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KQ030486.1 399265 2782756525 60 61
|
| 86 |
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KQ030487.1 316842 2783162470 60 61
|
| 87 |
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KZ289070.1 378870 2783484618 60 61
|
| 88 |
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KZ289084.1 283434 2783869828 60 61
|
| 89 |
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KZ289085.1 380404 2784158011 60 61
|
| 90 |
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KZ289093.1 245130 2784544781 60 61
|
| 91 |
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KZ289094.1 155470 2784794022 60 61
|
| 92 |
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KZ289095.1 305464 2784952109 60 61
|
| 93 |
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KZ289090.1 263917 2785262690 60 61
|
| 94 |
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KZ289091.1 448905 2785531031 60 61
|
| 95 |
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KZ289065.1 171653 2785987443 60 61
|
| 96 |
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KZ289064.1 117769 2786161982 60 61
|
| 97 |
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KB469739.1 331111 2786281739 60 61
|
| 98 |
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KB469741.2 505876 2786618401 60 61
|
| 99 |
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JH792829.1 352455 2787132734 60 61
|
| 100 |
+
KV575236.1 166096 2787491089 60 61
|
| 101 |
+
KV575233.1 266016 2787659979 60 61
|
| 102 |
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JH792826.1 368286 2787930454 60 61
|
| 103 |
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KZ289071.1 355613 2788304904 60 61
|
| 104 |
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JH792828.1 473738 2788666469 60 61
|
| 105 |
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KZ289083.1 66290 2789148128 60 61
|
| 106 |
+
KB469740.1 316140 2789215548 60 61
|
| 107 |
+
KZ289087.1 253113 2789536982 60 61
|
| 108 |
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KZ289089.1 662433 2789794339 60 61
|
| 109 |
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JH792832.1 544189 2790467838 60 61
|
| 110 |
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JH792833.1 221588 2791021122 60 61
|
| 111 |
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JH792827.1 205713 2791246429 60 61
|
| 112 |
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JH792834.1 331480 2791455596 60 61
|
| 113 |
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JH792831.2 203377 2791792626 60 61
|
| 114 |
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KB469742.1 1059955 2791999425 60 61
|
| 115 |
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KZ289067.1 583977 2793077071 60 61
|
| 116 |
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KQ030484.1 214957 2793670806 60 61
|
| 117 |
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KQ030494.1 506812 2793889371 60 61
|
| 118 |
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KQ030496.1 260447 2794404655 60 61
|
| 119 |
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KQ030497.1 219721 2794669468 60 61
|
| 120 |
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KQ030492.1 166012 2794892877 60 61
|
| 121 |
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KQ030493.2 423369 2795061681 60 61
|
| 122 |
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KQ030491.1 129865 2795492132 60 61
|
| 123 |
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KQ030488.1 45901 2795624187 60 61
|
| 124 |
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KQ030489.1 188269 2795670879 60 61
|
| 125 |
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KV575232.1 200008 2795862311 60 61
|
| 126 |
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KV575241.1 211337 2796065678 60 61
|
| 127 |
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KZ289076.1 318915 2796280563 60 61
|
| 128 |
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KZ289068.1 532572 2796604826 60 61
|
| 129 |
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KZ289069.1 709099 2797146298 60 61
|
| 130 |
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KV575242.1 299789 2797867239 60 61
|
| 131 |
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KZ289086.1 542789 2798172048 60 61
|
| 132 |
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KZ289066.1 339234 2798723907 60 61
|
| 133 |
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KK082441.1 456798 2799068829 60 61
|
| 134 |
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KZ289077.1 186144 2799533274 60 61
|
| 135 |
+
KZ289078.1 390920 2799722554 60 61
|
| 136 |
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KZ289079.1 368967 2800120023 60 61
|
| 137 |
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KZ289073.1 215264 2800495173 60 61
|
| 138 |
+
KZ289074.1 394026 2800714058 60 61
|
| 139 |
+
KZ289075.1 322221 2801114685 60 61
|
reference/MUS_MUSCULUS/gencode.vM23.annotation.gtf.gz.feather
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c9681e84f76384e1157b17d5e576dc0b35aaa4bc08b0f08e42881345c164d381
|
| 3 |
+
size 239017394
|
reference/MUS_MUSCULUS/gencode.vM38.splice_sites_ends.feather
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:761d560f0e0244306c9f34072be3753638f1f5e2a7639ade7614f6f3b370c615
|
| 3 |
+
size 5254098
|
reference/MUS_MUSCULUS/gencode.vM38.splice_sites_starts.feather
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:293e16dc5bf1e5220c2f75b30dc6633536b7f83352541fec1bd04b4063481b81
|
| 3 |
+
size 5155426
|
scripts/validate_dataset.py
ADDED
|
@@ -0,0 +1,79 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/usr/bin/env python3
|
| 2 |
+
"""Validate AlphaGenome dataset layout, checksums, and minimal readability."""
|
| 3 |
+
|
| 4 |
+
from __future__ import annotations
|
| 5 |
+
|
| 6 |
+
import argparse
|
| 7 |
+
import gzip
|
| 8 |
+
import hashlib
|
| 9 |
+
from pathlib import Path
|
| 10 |
+
import sys
|
| 11 |
+
|
| 12 |
+
import yaml
|
| 13 |
+
|
| 14 |
+
|
| 15 |
+
def sha256_file(path: Path) -> str:
|
| 16 |
+
digest = hashlib.sha256()
|
| 17 |
+
with path.open("rb") as f:
|
| 18 |
+
for chunk in iter(lambda: f.read(1024 * 1024), b""):
|
| 19 |
+
digest.update(chunk)
|
| 20 |
+
return digest.hexdigest()
|
| 21 |
+
|
| 22 |
+
|
| 23 |
+
def load_manifest(path: Path) -> dict:
|
| 24 |
+
return yaml.safe_load(path.read_text(encoding="utf-8"))
|
| 25 |
+
|
| 26 |
+
|
| 27 |
+
def validate_entry(root: Path, entry: dict, check_sha256: bool) -> None:
|
| 28 |
+
rel_path = entry["path"]
|
| 29 |
+
path = root / rel_path
|
| 30 |
+
if not path.is_file():
|
| 31 |
+
raise FileNotFoundError(f"missing file: {rel_path}")
|
| 32 |
+
size = path.stat().st_size
|
| 33 |
+
if size != int(entry["size_bytes"]):
|
| 34 |
+
raise ValueError(f"size mismatch for {rel_path}: {size} != {entry['size_bytes']}")
|
| 35 |
+
expected = entry.get("sha256")
|
| 36 |
+
if check_sha256 and expected:
|
| 37 |
+
actual = sha256_file(path)
|
| 38 |
+
if actual != expected:
|
| 39 |
+
raise ValueError(f"sha256 mismatch for {rel_path}: {actual} != {expected}")
|
| 40 |
+
if rel_path.endswith(".gz.tfrecord"):
|
| 41 |
+
with gzip.open(path, "rb") as f:
|
| 42 |
+
if not f.read(1):
|
| 43 |
+
raise ValueError(f"gzip TFRecord is unreadable: {rel_path}")
|
| 44 |
+
|
| 45 |
+
|
| 46 |
+
def main() -> int:
|
| 47 |
+
parser = argparse.ArgumentParser()
|
| 48 |
+
parser.add_argument("--root", default=".", help="dataset package root")
|
| 49 |
+
parser.add_argument(
|
| 50 |
+
"--manifest",
|
| 51 |
+
default="metadata/file_manifest.yaml",
|
| 52 |
+
help="file manifest relative to --root",
|
| 53 |
+
)
|
| 54 |
+
parser.add_argument(
|
| 55 |
+
"--check-sha256",
|
| 56 |
+
action="store_true",
|
| 57 |
+
help="verify full SHA256 for every listed file",
|
| 58 |
+
)
|
| 59 |
+
args = parser.parse_args()
|
| 60 |
+
|
| 61 |
+
root = Path(args.root).resolve()
|
| 62 |
+
manifest = load_manifest(root / args.manifest)
|
| 63 |
+
entries = manifest["files"]
|
| 64 |
+
for entry in entries:
|
| 65 |
+
validate_entry(root, entry, args.check_sha256)
|
| 66 |
+
|
| 67 |
+
print("dataset_validation_ok: true")
|
| 68 |
+
print(f"checked_files: {len(entries)}")
|
| 69 |
+
print(f"total_size_bytes: {sum(int(e['size_bytes']) for e in entries)}")
|
| 70 |
+
print("full_sha256_checked:", bool(args.check_sha256))
|
| 71 |
+
return 0
|
| 72 |
+
|
| 73 |
+
|
| 74 |
+
if __name__ == "__main__":
|
| 75 |
+
try:
|
| 76 |
+
raise SystemExit(main())
|
| 77 |
+
except Exception as exc:
|
| 78 |
+
print(f"dataset_validation_ok: false\nerror: {exc}", file=sys.stderr)
|
| 79 |
+
raise SystemExit(1)
|
v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_01-25.gz.tfrecord
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:d07c75e597927ec55eec05b1f56f97f098ea1519a0f97b499730cb06b763554b
|
| 3 |
+
size 293793071
|
v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_02-25.gz.tfrecord
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:d33fd3c5606f23d1f5fd90d7c52604fbcb88e6678e64d59d0658e900a9512e12
|
| 3 |
+
size 304275223
|
v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_03-25.gz.tfrecord
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:41c4ce54ae8841650b08c9c50f942d2e0bf9116107809df23af3a0a7569c861d
|
| 3 |
+
size 295604001
|
v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_04-25.gz.tfrecord
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a32b7f6f4795daae54d399e2a735679a7da356cd27ecc78c3e75374edbdfb6d1
|
| 3 |
+
size 287819663
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