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+v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/SPLICE_SITE_POSITIONS/data_chrAll_14-25.gz.tfrecord filter=lfs diff=lfs merge=lfs -text +v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/SPLICE_SITE_USAGE/data_chrAll_19-25.gz.tfrecord filter=lfs diff=lfs merge=lfs -text + +v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/SPLICE_SITE_USAGE/data_chrAll_25-25.gz.tfrecord filter=lfs diff=lfs merge=lfs -text \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..45744958542d39729502224b216b5aafe9173f1e --- /dev/null +++ b/README.md @@ -0,0 +1,86 @@ +--- +license: other +tags: + - GRCh38 + - GRCm38 +language: + - en + - zh +--- +

+ + AlphaGenome Dataset + +

+ +## Dataset Description + +AlphaGenome Dataset is a curated package of reference genomes, annotation files, and TFRecord data for use with the OneScience AlphaGenome model. + +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. + +## Supported Tasks + +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. + +## Dataset Format and Structure + +TFRecord file paths follow this pattern: + +```text +v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID//data_chrAll_01-25.gz.tfrecord +``` + +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. + +## How to Use the Dataset + +### Files and Download + +Standalone download: + +```bash +hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir . +``` + +Use within the model package: + +```bash +hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir data/alphagenome_dataset +``` + +### Data Placement and Validation + +When used as a model dependency, the following directory structure is recommended: + +```text +/data/alphagenome_dataset/ +├── manifest.yaml +├── metadata/ +├── reference/ +└── v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ +``` + +Quickly validate file presence, sizes, and gzip readability: + +```bash +python scripts/validate_dataset.py --root . +``` + +Add `--check-sha256` to perform a complete SHA256 validation. + +## Official OneScience Information + +| Platform | OneScience Main Repository | Skills Repository | +|---|---|---| +| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills | +| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills | + +## Limitations and License + +license: mixed +license_note: > + AlphaGenome training, validation and test datasets contain reprocessed + data from FANTOM5, 4D Nucleome, ENCODE and GENCODE. Usage is subject + to the respective source-specific licenses and data-use policies. + Other unspecified materials are licensed under CC BY-NC 4.0. \ No newline at end of file diff --git a/README_zh.md b/README_zh.md new file mode 100644 index 0000000000000000000000000000000000000000..c74ae752b58890d42e35e01b22615b6168bd30ca --- /dev/null +++ b/README_zh.md @@ -0,0 +1,86 @@ +--- +license: other +tags: + - GRCh38 + - GRCm38 +language: + - en + - zh +--- +

+ + AlphaGenome Dataset + +

+ +## 数据集描述 + +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。 + +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。 + +## 数据集支持的任务 + +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。 + +## 数据集的格式和结构 + +TFRecord 文件路径形如： + +```text +v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID//data_chrAll_01-25.gz.tfrecord +``` + +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`。 + +## 数据集使用方式 + +### 文件与下载 + +独立下载： + +```bash +hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir . +``` + +在模型包内使用： + +```bash +hf download --dataset OneScience-Sugon/alphagenome_dataset --local-dir data/alphagenome_dataset +``` + +### 数据放置与验证 + +作为模型依赖使用时，推荐目录结构： + +```text +/data/alphagenome_dataset/ +├── manifest.yaml +├── metadata/ +├── reference/ +└── v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ +``` + +快速验证文件存在、大小和 gzip 可读性： + +```bash +python scripts/validate_dataset.py --root . +``` + +全量 SHA256 验证可加 `--check-sha256`。 + +## OneScience 官方信息 + +| 平台 | OneScience 主仓库 | Skills 仓库 | +|---|---|---| +| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills | +| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills | + +## 限制与许可证 + +license: mixed +license_note: > + AlphaGenome training, validation and test datasets contain reprocessed + data from FANTOM5, 4D Nucleome, ENCODE and GENCODE. Usage is subject + to the respective source-specific licenses and data-use policies. + Other unspecified materials are licensed under CC BY-NC 4.0. \ No newline at end of file diff --git a/fasttrans-client.tar.gz b/fasttrans-client.tar.gz new file mode 100644 index 0000000000000000000000000000000000000000..f06204f4d53073d42981264564ed60d75500f851 --- /dev/null +++ b/fasttrans-client.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef4592c4701073b96e166f533364cb049be7e1ebbd093254fcac4ce4847140f2 +size 30145032 diff --git a/fasttrans/install_rayfile.sh b/fasttrans/install_rayfile.sh new file mode 100644 index 0000000000000000000000000000000000000000..e0676a2ea302269ea842b17fb7fb1307362f9d74 --- /dev/null +++ b/fasttrans/install_rayfile.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +if ! type rayfile-c >/dev/null 2>&1; then + raytar="rayfile-c" + folder="/usr/local/rayfile" + if [ ! -d ${folder} ]; then + mkdir ${folder} + fi + cp -f ${raytar} ${folder} > /dev/null 2>&1 + cp -f ${raytar} /usr/local/bin > /dev/null 2>&1 + echo "Rayfile client installed successfully!" +else + echo "Rayfile client already installed! You can try 'rayfile-c'" +fi diff --git a/fasttrans/rayfile-c b/fasttrans/rayfile-c new file mode 100644 index 0000000000000000000000000000000000000000..db87015f8625f6ebe8af2d6ff4b1875e9c8fb5de --- /dev/null +++ b/fasttrans/rayfile-c @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f718db7def476df9cdb259e0424b54bb0d0f82ed864adb84c62730b73d01b0a7 +size 111146248 diff --git a/fasttrans/readme.txt b/fasttrans/readme.txt new file mode 100644 index 0000000000000000000000000000000000000000..49fff026b1a97683215fb81ad49ac914c04a8481 --- /dev/null +++ b/fasttrans/readme.txt @@ -0,0 +1,5 @@ +1、请上传安装包fasttrans-client.tar.gz到linux服务器 +2、解压安装包：tar -zxf fasttrans-client.tar.gz +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、如果想在任意目录执行rayfile-c，需要root权限用户执行install_rayfile.sh + diff --git a/manifest.yaml b/manifest.yaml new file mode 100644 index 0000000000000000000000000000000000000000..77ec51189366a134e0c00341e4c579eaffd68661 --- /dev/null +++ b/manifest.yaml @@ -0,0 +1,291 @@ +onescience_manifest_version: "0.1" +resource_type: dataset +resource: + id: OneScience/alphagenome_dataset + name: AlphaGenome Dataset + domain: bio + domain_tags: [bio, genomics, regulatory_genomics] + task: regulatory_genomics_training_and_evaluation + task_tags: [reference_genome, tfrecord, evaluation, training] + modalities: [dna_sequence, functional_genomics_tracks, variants] + input_formats: [fasta, fai, feather, tfrecord] + output_formats: [] + 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。 + +platform_resource: + primary: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset + revision: main + readme_path: README.md + manifest_path: manifest.yaml + mirrors: [] + access: + visibility: public + license: alphagenome-dataset-terms + +website_integration: + enabled: true + click_target: + platform: modelscope + resource_url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset + llm_handoff: + readme_required: true + manifest_required: true + download_readme_first: true + resolve_related_models: true + default_run_goal: dataset_validation + +runtime: + enabled: true + onescience_domain: bio + min_onescience_version: null + supported_execution: [local, local_slurm, remote_slurm, scnet_mcp] + +onescience: + repo: https://gitee.com/onescience-ai/onescience + official_links: + gitee: + doc: https://gitee.com/onescience-ai/onescience-doc + onescience: https://gitee.com/onescience-ai/onescience + skills: https://gitee.com/onescience-ai/oneskills + github: + doc: https://github.com/onescience-ai/OneScience-doc + onescience: https://github.com/onescience-ai/OneScience + skills: https://github.com/onescience-ai/oneskills + install: + required_by_default: false + command: bash install.sh bio + source_paths: + - src/onescience/flax_models/alphagenome/io/dataset.py + compatibility: + examples_path: examples/biosciences/alphagenome + status: examples_compatible + +runtime_package: + kind: standard_runtime_package + package_root: . + standard_layout: + workdir: . + config_dir: metadata + checkpoint_dir: null + data_dir: . + output_dir: validation_outputs + apply_policy: + mode: direct_use + target: session_data_dir + overwrite: true + protect_installed_onescience: true + entry_files: + - metadata/schema.yaml + - metadata/file_manifest.yaml + - scripts/validate_dataset.py + entrypoints: + preflight: scripts/validate_dataset.py + inference: null + train: null + finetune: null + evaluate: null + visualize: null + deploy: null + +files: + dataset_files: + - id: file_manifest + path: metadata/file_manifest.yaml + role: integrity_manifest + format: yaml + 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。 + required: true + required_for: [preflight, train, evaluate, inference] + source: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + path: metadata/file_manifest.yaml + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: metadata/file_manifest.yaml + - id: schema + path: metadata/schema.yaml + role: schema + format: yaml + description_zh: 描述 TFRecord bundle、tensor dtype、参考基因组和可用 split。 + required: true + required_for: [preflight, train, evaluate] + local_path: metadata/schema.yaml + - id: reference_genomes + path: reference/ + role: reference_genome + format: fasta_fai_feather + 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。 + required: true + required_for: [preflight, inference, variant_scoring] + source: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + path: reference/ + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: reference/ + - id: valid_tfrecords + path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + role: evaluation_data + format: gzipped_tfrecord + description_zh: HOMO_SAPIENS ALL_FOLDS VALID split，12 个 bundle，每个 bundle 25 个 gzipped TFRecord 分片。 + required: true + required_for: [preflight, evaluate] + source: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + - id: fasttrans_tools + path: fasttrans/ + role: transfer_tool + format: binary + 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。 + required: false + required_for: [] + local_path: fasttrans/ + config_files: [] + sample_files: [] + script_files: + - id: validate_dataset + path: scripts/validate_dataset.py + role: preflight + description_zh: 根据 metadata/file_manifest.yaml 校验文件名、大小、可选 SHA256 和 TFRecord gzip 可读性。 + required: true + required_for: [preflight] + +dataset: + format: [gzipped_tfrecord, fasta, fai, feather] + 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。 + schema: + path: metadata/schema.yaml + integrity_manifest: + path: metadata/file_manifest.yaml + file_count: 315 + includes_sha256: true + splits: + train: null + validation: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + test: null + +relations: + required_datasets: [] + optional_datasets: [] + compatible_models: + - id: OneScience/alphagenome/ + role: reference_and_eval_data + required_for: [preflight, inference, variant_scoring, evaluate] + resource_ref: + platform: modelscope + repo_id: OneScience/alphagenome/ + repo_type: model + url: https://modelscope.cn/models/OneScience/alphagenome/ + revision: main + readme_path: README.md + manifest_path: manifest.yaml + expected_local_path: data/alphagenome_dataset + adapter: null + +run_matrix: + scenarios: + - name: dataset_validation + default: true + goal: minimal_validation + required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords] + required_model_files: [] + required_datasets: [] + command_refs: [commands.preflight.validate_dataset_fast] + outputs: [dataset_validation_stdout] + prerequisites: + - cwd 为数据集包根目录。 + - name: dataset_validation_full_sha256 + goal: integrity_validation + required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords] + required_model_files: [] + required_datasets: [] + command_refs: [commands.preflight.validate_dataset_full_sha256] + outputs: [dataset_validation_stdout] + prerequisites: + - cwd 为数据集包根目录。 + - 允许读取全部 114G 数据计算 SHA256。 + +capabilities: + inference: false + train: true + finetune: true + evaluate: true + visualize: false + deploy: false + +commands: + download: + - name: download_dataset + cwd: . + command: modelscope download --dataset OneScience/alphagenome_dataset --local_dir . + description_zh: 下载 AlphaGenome 数据集包到当前目录。 + preflight: + - name: validate_dataset_fast + cwd: . + command: python scripts/validate_dataset.py --root . + description_zh: 快速校验文件存在、大小一致并抽查 TFRecord gzip 可读性。 + - name: validate_dataset_full_sha256 + cwd: . + command: python scripts/validate_dataset.py --root . --check-sha256 + description_zh: 全量校验文件名、大小和 SHA256，耗时取决于存储带宽。 + prepare: [] + inference: [] + train: [] + finetune: [] + evaluate: [] + visualize: [] + deploy: [] + +expected_outputs: + - id: dataset_validation_stdout + path: stdout + description_zh: "输出 dataset_validation_ok: true、checked_files 和 total_size_bytes。" + +diagnostics: + - id: missing_file + match: "missing file" + severity: error + message_zh: 数据文件缺失。 + 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。 + - id: size_mismatch + match: "size mismatch" + severity: error + message_zh: 整理后文件大小与原始清单不一致。 + 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。 + - id: sha256_mismatch + match: "sha256 mismatch" + severity: error + message_zh: 文件内容与原始清单不一致。 + fix_zh: 重新下载对应文件并再次执行全量 SHA256 校验。 + - id: gzip_unreadable + match: "gzip TFRecord is unreadable" + severity: error + message_zh: TFRecord gzip 压缩流无法读取。 + fix_zh: 重新下载对应 TFRecord 分片。 + +domain_extension: + bio: + organisms: [HOMO_SAPIENS, MUS_MUSCULUS] + genome_builds: + HOMO_SAPIENS: GRCh38.p13 + MUS_MUSCULUS: GRCm38.p6 + available_split: ALL_FOLDS/HOMO_SAPIENS/VALID + bundle_count: 12 + shards_per_bundle: 25 diff --git a/metadata/file_manifest.yaml b/metadata/file_manifest.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d58889369b2f02ac674e0dd3ee9a096ac2c7b3c6 --- /dev/null +++ b/metadata/file_manifest.yaml @@ -0,0 +1,1263 @@ +source_root: /public/share/sugonhpcapp01/onestore/onedatasets/AlphaGenome +file_count: 315 +files: +- path: fasttrans/install_rayfile.sh + source_path: /public/share/sugonhpcapp01/onestore/onedatasets/AlphaGenome/fasttrans/install_rayfile.sh + size_bytes: 379 + sha256: f612f43730e1c3f00f0fdcc5089786d5d06315b9a5057734571df0551557ece9 +- path: fasttrans/rayfile-c + 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b/metadata/schema.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ff47fd8f03e54cc340847c90326f3075d4e870a8 --- /dev/null +++ b/metadata/schema.yaml @@ -0,0 +1,71 @@ +dataset: AlphaGenome +repo_id: OneScience/alphagenome_dataset +format: + - gzipped TFRecord + - FASTA + - FASTA index + - feather +organisms: + - HOMO_SAPIENS + - MUS_MUSCULUS +splits: + available: + - ALL_FOLDS/HOMO_SAPIENS/VALID +bundles: + ATAC: + tensors: + atac: bfloat16 + atac_mask: bool + resolution_bp: 1 + DNASE: + tensors: + dnase: bfloat16 + dnase_mask: bool + resolution_bp: 1 + CAGE: + tensors: + cage: bfloat16 + cage_mask: bool + resolution_bp: 1 + RNA_SEQ: + tensors: + rna_seq: bfloat16 + rna_seq_mask: bool + rna_seq_strand: int32 + resolution_bp: 1 + CHIP_TF: + tensors: + chip_tf: float32 + chip_tf_mask: bool + resolution_bp: 128 + CHIP_HISTONE: + tensors: + chip_histone: float32 + chip_histone_mask: bool + resolution_bp: 128 + CONTACT_MAPS: + tensors: + contact_maps: float32 + resolution_bp: 2048 + PROCAP: + tensors: + procap: bfloat16 + procap_mask: bool + resolution_bp: 1 + SPLICE_SITES: + tensors: + splice_sites: bool + resolution_bp: 1 + SPLICE_SITE_USAGE: + tensors: + splice_site_usage: float16 + resolution_bp: 1 + SPLICE_JUNCTIONS: + tensors: + splice_junctions: float32 + resolution_bp: 1 + SPLICE_SITE_POSITIONS: + tensors: + splice_site_positions: int32 + resolution_bp: 1 +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。 diff --git a/onescience_run_manifest.yaml b/onescience_run_manifest.yaml new file mode 100644 index 0000000000000000000000000000000000000000..77ec51189366a134e0c00341e4c579eaffd68661 --- /dev/null +++ b/onescience_run_manifest.yaml @@ -0,0 +1,291 @@ +onescience_manifest_version: "0.1" +resource_type: dataset +resource: + id: OneScience/alphagenome_dataset + name: AlphaGenome Dataset + domain: bio + domain_tags: [bio, genomics, regulatory_genomics] + task: regulatory_genomics_training_and_evaluation + task_tags: [reference_genome, tfrecord, evaluation, training] + modalities: [dna_sequence, functional_genomics_tracks, variants] + input_formats: [fasta, fai, feather, tfrecord] + output_formats: [] + 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。 + +platform_resource: + primary: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset + revision: main + readme_path: README.md + manifest_path: manifest.yaml + mirrors: [] + access: + visibility: public + license: alphagenome-dataset-terms + +website_integration: + enabled: true + click_target: + platform: modelscope + resource_url: https://modelscope.cn/datasets/OneScience/alphagenome_dataset + llm_handoff: + readme_required: true + manifest_required: true + download_readme_first: true + resolve_related_models: true + default_run_goal: dataset_validation + +runtime: + enabled: true + onescience_domain: bio + min_onescience_version: null + supported_execution: [local, local_slurm, remote_slurm, scnet_mcp] + +onescience: + repo: https://gitee.com/onescience-ai/onescience + official_links: + gitee: + doc: https://gitee.com/onescience-ai/onescience-doc + onescience: https://gitee.com/onescience-ai/onescience + skills: https://gitee.com/onescience-ai/oneskills + github: + doc: https://github.com/onescience-ai/OneScience-doc + onescience: https://github.com/onescience-ai/OneScience + skills: https://github.com/onescience-ai/oneskills + install: + required_by_default: false + command: bash install.sh bio + source_paths: + - src/onescience/flax_models/alphagenome/io/dataset.py + compatibility: + examples_path: examples/biosciences/alphagenome + status: examples_compatible + +runtime_package: + kind: standard_runtime_package + package_root: . + standard_layout: + workdir: . + config_dir: metadata + checkpoint_dir: null + data_dir: . + output_dir: validation_outputs + apply_policy: + mode: direct_use + target: session_data_dir + overwrite: true + protect_installed_onescience: true + entry_files: + - metadata/schema.yaml + - metadata/file_manifest.yaml + - scripts/validate_dataset.py + entrypoints: + preflight: scripts/validate_dataset.py + inference: null + train: null + finetune: null + evaluate: null + visualize: null + deploy: null + +files: + dataset_files: + - id: file_manifest + path: metadata/file_manifest.yaml + role: integrity_manifest + format: yaml + 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。 + required: true + required_for: [preflight, train, evaluate, inference] + source: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + path: metadata/file_manifest.yaml + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: metadata/file_manifest.yaml + - id: schema + path: metadata/schema.yaml + role: schema + format: yaml + description_zh: 描述 TFRecord bundle、tensor dtype、参考基因组和可用 split。 + required: true + required_for: [preflight, train, evaluate] + local_path: metadata/schema.yaml + - id: reference_genomes + path: reference/ + role: reference_genome + format: fasta_fai_feather + 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。 + required: true + required_for: [preflight, inference, variant_scoring] + source: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + path: reference/ + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: reference/ + - id: valid_tfrecords + path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + role: evaluation_data + format: gzipped_tfrecord + description_zh: HOMO_SAPIENS ALL_FOLDS VALID split，12 个 bundle，每个 bundle 25 个 gzipped TFRecord 分片。 + required: true + required_for: [preflight, evaluate] + source: + platform: modelscope + repo_id: OneScience/alphagenome_dataset + repo_type: dataset + path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + revision: main + download_method: command_ref + command_ref: commands.download.download_dataset + local_path: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + - id: fasttrans_tools + path: fasttrans/ + role: transfer_tool + format: binary + 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。 + required: false + required_for: [] + local_path: fasttrans/ + config_files: [] + sample_files: [] + script_files: + - id: validate_dataset + path: scripts/validate_dataset.py + role: preflight + description_zh: 根据 metadata/file_manifest.yaml 校验文件名、大小、可选 SHA256 和 TFRecord gzip 可读性。 + required: true + required_for: [preflight] + +dataset: + format: [gzipped_tfrecord, fasta, fai, feather] + 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。 + schema: + path: metadata/schema.yaml + integrity_manifest: + path: metadata/file_manifest.yaml + file_count: 315 + includes_sha256: true + splits: + train: null + validation: v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ + test: null + +relations: + required_datasets: [] + optional_datasets: [] + compatible_models: + - id: OneScience/alphagenome/ + role: reference_and_eval_data + required_for: [preflight, inference, variant_scoring, evaluate] + resource_ref: + platform: modelscope + repo_id: OneScience/alphagenome/ + repo_type: model + url: https://modelscope.cn/models/OneScience/alphagenome/ + revision: main + readme_path: README.md + manifest_path: manifest.yaml + expected_local_path: data/alphagenome_dataset + adapter: null + +run_matrix: + scenarios: + - name: dataset_validation + default: true + goal: minimal_validation + required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords] + required_model_files: [] + required_datasets: [] + command_refs: [commands.preflight.validate_dataset_fast] + outputs: [dataset_validation_stdout] + prerequisites: + - cwd 为数据集包根目录。 + - name: dataset_validation_full_sha256 + goal: integrity_validation + required_dataset_files: [file_manifest, schema, reference_genomes, valid_tfrecords] + required_model_files: [] + required_datasets: [] + command_refs: [commands.preflight.validate_dataset_full_sha256] + outputs: [dataset_validation_stdout] + prerequisites: + - cwd 为数据集包根目录。 + - 允许读取全部 114G 数据计算 SHA256。 + +capabilities: + inference: false + train: true + finetune: true + evaluate: true + visualize: false + deploy: false + +commands: + download: + - name: download_dataset + cwd: . + command: modelscope download --dataset OneScience/alphagenome_dataset --local_dir . + description_zh: 下载 AlphaGenome 数据集包到当前目录。 + preflight: + - name: validate_dataset_fast + cwd: . + command: python scripts/validate_dataset.py --root . + description_zh: 快速校验文件存在、大小一致并抽查 TFRecord gzip 可读性。 + - name: validate_dataset_full_sha256 + cwd: . + command: python scripts/validate_dataset.py --root . --check-sha256 + description_zh: 全量校验文件名、大小和 SHA256，耗时取决于存储带宽。 + prepare: [] + inference: [] + train: [] + finetune: [] + evaluate: [] + visualize: [] + deploy: [] + +expected_outputs: + - id: dataset_validation_stdout + path: stdout + description_zh: "输出 dataset_validation_ok: true、checked_files 和 total_size_bytes。" + +diagnostics: + - id: missing_file + match: "missing file" + severity: error + message_zh: 数据文件缺失。 + 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。 + - id: size_mismatch + match: "size mismatch" + severity: error + message_zh: 整理后文件大小与原始清单不一致。 + 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。 + - id: sha256_mismatch + match: "sha256 mismatch" + severity: error + message_zh: 文件内容与原始清单不一致。 + fix_zh: 重新下载对应文件并再次执行全量 SHA256 校验。 + - id: gzip_unreadable + match: "gzip TFRecord is unreadable" + severity: error + message_zh: TFRecord gzip 压缩流无法读取。 + fix_zh: 重新下载对应 TFRecord 分片。 + +domain_extension: + bio: + organisms: [HOMO_SAPIENS, MUS_MUSCULUS] + genome_builds: + HOMO_SAPIENS: GRCh38.p13 + MUS_MUSCULUS: GRCm38.p6 + available_split: 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annotations + +import argparse +import gzip +import hashlib +from pathlib import Path +import sys + +import yaml + + +def sha256_file(path: Path) -> str: + digest = hashlib.sha256() + with path.open("rb") as f: + for chunk in iter(lambda: f.read(1024 * 1024), b""): + digest.update(chunk) + return digest.hexdigest() + + +def load_manifest(path: Path) -> dict: + return yaml.safe_load(path.read_text(encoding="utf-8")) + + +def validate_entry(root: Path, entry: dict, check_sha256: bool) -> None: + rel_path = entry["path"] + path = root / rel_path + if not path.is_file(): + raise FileNotFoundError(f"missing file: {rel_path}") + size = path.stat().st_size + if size != int(entry["size_bytes"]): + raise ValueError(f"size mismatch for {rel_path}: {size} != {entry['size_bytes']}") + expected = entry.get("sha256") + if check_sha256 and expected: + actual = sha256_file(path) + if actual != expected: + raise ValueError(f"sha256 mismatch for {rel_path}: {actual} != {expected}") + if rel_path.endswith(".gz.tfrecord"): + with gzip.open(path, "rb") as f: + if not f.read(1): + raise ValueError(f"gzip TFRecord is unreadable: {rel_path}") + + +def main() -> int: + parser = argparse.ArgumentParser() + parser.add_argument("--root", default=".", help="dataset package root") + parser.add_argument( + "--manifest", + default="metadata/file_manifest.yaml", + help="file manifest relative to --root", + ) + parser.add_argument( + "--check-sha256", + action="store_true", + help="verify full SHA256 for every listed file", + ) + args = parser.parse_args() + + root = Path(args.root).resolve() + manifest = load_manifest(root / args.manifest) + entries = manifest["files"] + for entry in entries: + validate_entry(root, entry, args.check_sha256) + + print("dataset_validation_ok: true") + print(f"checked_files: {len(entries)}") + print(f"total_size_bytes: {sum(int(e['size_bytes']) for e in entries)}") + print("full_sha256_checked:", bool(args.check_sha256)) + return 0 + + +if __name__ == "__main__": + try: + raise SystemExit(main()) + except Exception as exc: + print(f"dataset_validation_ok: false\nerror: {exc}", file=sys.stderr) + raise SystemExit(1) diff --git a/v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_01-25.gz.tfrecord b/v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_01-25.gz.tfrecord new file mode 100644 index 0000000000000000000000000000000000000000..e610c72ef29baea83300bccee8ab9ab558c874c6 --- /dev/null +++ b/v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_01-25.gz.tfrecord @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d07c75e597927ec55eec05b1f56f97f098ea1519a0f97b499730cb06b763554b +size 293793071 diff --git a/v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_02-25.gz.tfrecord b/v1/train/ALL_FOLDS/HOMO_SAPIENS/VALID/ATAC/data_chrAll_02-25.gz.tfrecord new file mode 100644 index 0000000000000000000000000000000000000000..75885dba173f4b73fffbcf3322ef6eb84c1c4ddb --- /dev/null +++ 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