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"cells": [
{
"cell_type": "markdown",
"id": "overview",
"metadata": {},
"source": [
"# scPerturb 数据处理\n",
"\n",
"这个 notebook 先完成两件事：\n",
"\n",
"1. 统一展示当前 `.h5ad` 文件的结构。\n",
"2. 根据这些结构，自动提取一个后续建模可直接使用的标准化 metadata 表。"
]
},
{
"cell_type": "markdown",
"id": "workflow",
"metadata": {},
"source": [
"\n",
"\n",
"- 对比不同数据集的 `obs` 字段，确认 perturbation 标签列名\n",
"- 找到表达矩阵、原始矩阵和其他矩阵存储位置\n",
"- 统一提取每个细胞的 perturbation 信息\n",
"- 标记哪些细胞更接近单 perturbation"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "setup",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Kernel python: /opt/miniconda3/bin/python\n",
"Project root: /Users/yurujiang/Desktop/final_thesis\n",
"Search root: /Users/yurujiang/Desktop/final_thesis/data/scPerturb\n",
"Found 4 h5ad file(s).\n"
]
}
],
"source": [
"from __future__ import annotations\n",
"\n",
"from pathlib import Path\n",
"import re\n",
"import sys\n",
"\n",
"import pandas as pd\n",
"import anndata as ad\n",
"import h5py\n",
"\n",
"\n",
"def find_project_root(start: Path) -> Path:\n",
" for candidate in [start, *start.parents]:\n",
" if (candidate / \"src\").exists() and (candidate / \"data\").exists():\n",
" return candidate\n",
" return start\n",
"\n",
"\n",
"PROJECT_ROOT = find_project_root(Path.cwd().resolve())\n",
"H5AD_ROOT = PROJECT_ROOT / \"data\" / \"scPerturb\"\n",
"H5AD_FILES = sorted(H5AD_ROOT.rglob(\"*.h5ad\"))\n",
"\n",
"print(f\"Kernel python: {sys.executable}\")\n",
"print(f\"Project root: {PROJECT_ROOT}\")\n",
"print(f\"Search root: {H5AD_ROOT}\")\n",
"print(f\"Found {len(H5AD_FILES)} h5ad file(s).\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "list-files",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Available .h5ad files:\n",
"- data/scPerturb/rna_protein/AdamsonWeissman2016_GSM2406675_10X001.h5ad (32.96 MB)\n",
"- data/scPerturb/rna_protein/AdamsonWeissman2016_GSM2406677_10X005.h5ad (132.62 MB)\n",
"- data/scPerturb/rna_protein/AdamsonWeissman2016_GSM2406681_10X010.h5ad (449.45 MB)\n",
"- data/scPerturb/rna_protein/ReplogleWeissman2022_K562_essential.h5ad (1475.08 MB)\n"
]
}
],
"source": [
"if not H5AD_FILES:\n",
" print(\"No .h5ad files found under data/scPerturb/. Please run download.ipynb first.\")\n",
"else:\n",
" print(\"Available .h5ad files:\")\n",
" for path in H5AD_FILES:\n",
" rel_path = path.relative_to(PROJECT_ROOT)\n",
" size_mb = path.stat().st_size / 1024 / 1024\n",
" print(f\"- {rel_path} ({size_mb:.2f} MB)\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "hdf5-tree-helpers",
"metadata": {},
"outputs": [],
"source": [
"def _format_hdf5_node(node) -> str:\n",
" shape = getattr(node, \"shape\", None)\n",
" dtype = getattr(node, \"dtype\", None)\n",
" if shape is None:\n",
" return \"group\"\n",
" return f\"dataset shape={shape}, dtype={dtype}\"\n",
"\n",
"\n",
"def print_hdf5_tree(path: Path, max_depth: int = 2, max_children: int = 12) -> None:\n",
" print(f\"\\n=== HDF5 tree: {path.name} ===\")\n",
" with h5py.File(path, \"r\") as handle:\n",
" def walk(group, depth: int = 0, prefix: str = \"\"):\n",
" if depth > max_depth:\n",
" return\n",
"\n",
" items = list(group.items())\n",
" visible_items = items[:max_children]\n",
" for index, (name, node) in enumerate(visible_items):\n",
" connector = \"└── \" if index == len(visible_items) - 1 else \"├── \"\n",
" print(f\"{prefix}{connector}{name} [{_format_hdf5_node(node)}]\")\n",
" if hasattr(node, \"items\") and depth < max_depth:\n",
" extension = \" \" if index == len(visible_items) - 1 else \"│ \"\n",
" walk(node, depth + 1, prefix + extension)\n",
"\n",
" if len(items) > max_children:\n",
" print(f\"{prefix}... ({len(items) - max_children} more item(s) omitted)\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "show-hdf5-tree",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"=== HDF5 tree: AdamsonWeissman2016_GSM2406675_10X001.h5ad ===\n",
"\n",
"=== HDF5 tree: AdamsonWeissman2016_GSM2406677_10X005.h5ad ===\n",
"\n",
"=== HDF5 tree: AdamsonWeissman2016_GSM2406681_10X010.h5ad ===\n",
"\n",
"=== HDF5 tree: ReplogleWeissman2022_K562_essential.h5ad ===\n"
]
}
],
"source": [
"# 如需查看 HDF5 层级，可取消注释运行\n",
"for path in H5AD_FILES:\n",
" print_hdf5_tree(path, max_depth=2, max_children=12)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "anndata-summary-helpers",
"metadata": {},
"outputs": [],
"source": [
"def summarize_anndata(path: Path) -> None:\n",
" print(f\"\\n=== AnnData summary: {path.name} ===\")\n",
" adata = ad.read_h5ad(path, backed=\"r\")\n",
" try:\n",
" print(f\"shape: {adata.shape}\")\n",
" print(f\"obs columns ({len(adata.obs.columns)}): {list(adata.obs.columns)}\")\n",
" print(f\"var columns ({len(adata.var.columns)}): {list(adata.var.columns)}\")\n",
" print(f\"layers: {list(adata.layers.keys())}\")\n",
" print(f\"obsm: {list(adata.obsm.keys())}\")\n",
" print(f\"varm: {list(adata.varm.keys())}\")\n",
" print(f\"uns: {list(adata.uns.keys())}\")\n",
"\n",
" if len(adata.obs.columns) > 0:\n",
" print(\"obs head:\")\n",
" print(adata.obs.head(3))\n",
"\n",
" if len(adata.var.columns) > 0:\n",
" print(\"var head:\")\n",
" print(adata.var.head(3))\n",
" finally:\n",
" if getattr(adata, \"file\", None) is not None:\n",
" adata.file.close()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "show-anndata-summary",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"=== AnnData summary: AdamsonWeissman2016_GSM2406675_10X001.h5ad ===\n",
"shape: (5768, 35635)\n",
"obs columns (15): ['perturbation', 'read count', 'UMI count', 'tissue_type', 'cell_line', 'cancer', 'disease', 'perturbation_type', 'celltype', 'organism', 'ncounts', 'ngenes', 'percent_mito', 'percent_ribo', 'nperts']\n",
"var columns (3): ['ensembl_id', 'ncounts', 'ncells']\n",
"layers: []\n",
"obsm: []\n",
"varm: []\n",
"uns: []\n",
"obs head:\n",
" perturbation read count UMI count tissue_type cell_line \\\n",
"cell_barcode \n",
"AAACATACACCGAT CREB1_pDS269 1286.0 98.0 cell_line K562 \n",
"AAACATACAGAGAT SNAI1_pDS266 296.0 19.0 cell_line K562 \n",
"AAACATACCAGAAA 62(mod)_pBA581 1829.0 162.0 cell_line K562 \n",
"\n",
" cancer disease perturbation_type \\\n",
"cell_barcode \n",
"AAACATACACCGAT True chronic myelogenous leukemia CRISPR \n",
"AAACATACAGAGAT True chronic myelogenous leukemia CRISPR \n",
"AAACATACCAGAAA True chronic myelogenous leukemia CRISPR \n",
"\n",
" celltype organism ncounts ngenes percent_mito \\\n",
"cell_barcode \n",
"AAACATACACCGAT lymphoblasts human 8138.0 2412 0.0 \n",
"AAACATACAGAGAT lymphoblasts human 8980.0 2386 0.0 \n",
"AAACATACCAGAAA lymphoblasts human 28610.0 4404 0.0 \n",
"\n",
" percent_ribo nperts \n",
"cell_barcode \n",
"AAACATACACCGAT 34.037846 2 \n",
"AAACATACAGAGAT 40.011135 2 \n",
"AAACATACCAGAAA 40.003494 2 \n",
"var head:\n",
" ensembl_id ncounts ncells\n",
"gene_symbol \n",
"MIR1302-10 ENSG00000243485 0.0 0\n",
"FAM138A ENSG00000237613 0.0 0\n",
"OR4F5 ENSG00000186092 0.0 0\n",
"\n",
"=== AnnData summary: AdamsonWeissman2016_GSM2406677_10X005.h5ad ===\n",
"shape: (15006, 32738)\n",
"obs columns (15): ['perturbation', 'read count', 'UMI count', 'tissue_type', 'cell_line', 'cancer', 'disease', 'perturbation_type', 'celltype', 'organism', 'ncounts', 'ngenes', 'percent_mito', 'percent_ribo', 'nperts']\n",
"var columns (3): ['ensembl_id', 'ncounts', 'ncells']\n",
"layers: []\n",
"obsm: []\n",
"varm: []\n",
"uns: []\n",
"obs head:\n",
" perturbation read count UMI count tissue_type \\\n",
"cell_barcode \n",
"AAACATACACTCAG 3x_neg_ctrl_pMJ144-1 261.0 59.0 cell_line \n",
"AAACATACTCCTAT 3x_neg_ctrl_pMJ144-2 132.0 37.0 cell_line \n",
"AAACATTGCAGAGG 3x_neg_ctrl_pMJ144-2 560.0 117.0 cell_line \n",
"\n",
" cell_line cancer disease \\\n",
"cell_barcode \n",
"AAACATACACTCAG K562 True chronic myelogenous leukemia \n",
"AAACATACTCCTAT K562 True chronic myelogenous leukemia \n",
"AAACATTGCAGAGG K562 True chronic myelogenous leukemia \n",
"\n",
" perturbation_type celltype organism ncounts ngenes \\\n",
"cell_barcode \n",
"AAACATACACTCAG CRISPR lymphoblasts human 24343.0 4164 \n",
"AAACATACTCCTAT CRISPR lymphoblasts human 27678.0 4428 \n",
"AAACATTGCAGAGG CRISPR lymphoblasts human 24745.0 4371 \n",
"\n",
" percent_mito percent_ribo nperts \n",
"cell_barcode \n",
"AAACATACACTCAG 4.563941 32.629505 4 \n",
"AAACATACTCCTAT 4.508996 28.658140 4 \n",
"AAACATTGCAGAGG 3.200647 31.117397 4 \n",
"var head:\n",
" ensembl_id ncounts ncells\n",
"gene_symbol \n",
"MIR1302-10 ENSG00000243485 2.0 2\n",
"FAM138A ENSG00000237613 0.0 0\n",
"OR4F5 ENSG00000186092 0.0 0\n",
"\n",
"=== AnnData summary: AdamsonWeissman2016_GSM2406681_10X010.h5ad ===\n",
"shape: (65337, 32738)\n",
"obs columns (15): ['perturbation', 'read count', 'UMI count', 'tissue_type', 'cell_line', 'cancer', 'disease', 'perturbation_type', 'celltype', 'organism', 'ncounts', 'ngenes', 'percent_mito', 'percent_ribo', 'nperts']\n",
"var columns (3): ['ensembl_id', 'ncounts', 'ncells']\n",
"layers: []\n",
"obsm: []\n",
"varm: []\n",
"uns: []\n",
"obs head:\n",
" perturbation read count UMI count tissue_type cell_line \\\n",
"cell_barcode \n",
"AAACATACAAGATG 63(mod)_pBA580 282.0 8.0 cell_line K562 \n",
"AAACATACACCTAG OST4_pDS353 331.0 7.0 cell_line K562 \n",
"AAACATACTTCCCG SEC61A1_pDS031 285.0 10.0 cell_line K562 \n",
"\n",
" cancer disease perturbation_type \\\n",
"cell_barcode \n",
"AAACATACAAGATG True chronic myelogenous leukemia CRISPR \n",
"AAACATACACCTAG True chronic myelogenous leukemia CRISPR \n",
"AAACATACTTCCCG True chronic myelogenous leukemia CRISPR \n",
"\n",
" celltype organism ncounts ngenes percent_mito \\\n",
"cell_barcode \n",
"AAACATACAAGATG lymphoblasts human 8866.0 2914 4.917663 \n",
"AAACATACACCTAG lymphoblasts human 13785.0 3818 4.468626 \n",
"AAACATACTTCCCG lymphoblasts human 7569.0 2616 5.060113 \n",
"\n",
" percent_ribo nperts \n",
"cell_barcode \n",
"AAACATACAAGATG 21.306112 2 \n",
"AAACATACACCTAG 19.492201 2 \n",
"AAACATACTTCCCG 23.199894 2 \n",
"var head:\n",
" ensembl_id ncounts ncells\n",
"gene_symbol \n",
"MIR1302-10 ENSG00000243485 11.0 11\n",
"FAM138A ENSG00000237613 0.0 0\n",
"OR4F5 ENSG00000186092 0.0 0\n",
"\n",
"=== AnnData summary: ReplogleWeissman2022_K562_essential.h5ad ===\n",
"shape: (310385, 8563)\n",
"obs columns (24): ['batch', 'gene', 'gene_id', 'transcript', 'gene_transcript', 'guide_id', 'percent_mito', 'UMI_count', 'z_gemgroup_UMI', 'core_scale_factor', 'core_adjusted_UMI_count', 'disease', 'cancer', 'cell_line', 'sex', 'age', 'perturbation', 'organism', 'perturbation_type', 'tissue_type', 'ncounts', 'ngenes', 'nperts', 'percent_ribo']\n",
"var columns (14): ['chr', 'start', 'end', 'class', 'strand', 'length', 'in_matrix', 'mean', 'std', 'cv', 'fano', 'ensembl_id', 'ncounts', 'ncells']\n",
"layers: []\n",
"obsm: []\n",
"varm: []\n",
"uns: []\n",
"obs head:\n",
" batch gene gene_id transcript \\\n",
"cell_barcode \n",
"AAACCCAAGAAATCCA-27 27 NAF1 ENSG00000145414 P1P2 \n",
"AAACCCAAGAACTTCC-31 31 BUB1 ENSG00000169679 P1P2 \n",
"AAACCCAAGAAGCCAC-34 34 UBL5 ENSG00000198258 P1P2 \n",
"\n",
" gene_transcript \\\n",
"cell_barcode \n",
"AAACCCAAGAAATCCA-27 5449_NAF1_P1P2_ENSG00000145414 \n",
"AAACCCAAGAACTTCC-31 935_BUB1_P1P2_ENSG00000169679 \n",
"AAACCCAAGAAGCCAC-34 9534_UBL5_P1P2_ENSG00000198258 \n",
"\n",
" guide_id \\\n",
"cell_barcode \n",
"AAACCCAAGAAATCCA-27 NAF1_+_164087918.23-P1P2|NAF1_-_164087674.23-P1P2 \n",
"AAACCCAAGAACTTCC-31 BUB1_-_111435363.23-P1P2|BUB1_-_111435372.23-P1P2 \n",
"AAACCCAAGAAGCCAC-34 UBL5_-_9938639.23-P1P2|UBL5_+_9938801.23-P1P2 \n",
"\n",
" percent_mito UMI_count z_gemgroup_UMI \\\n",
"cell_barcode \n",
"AAACCCAAGAAATCCA-27 0.112083 11438.0 0.013047 \n",
"AAACCCAAGAACTTCC-31 0.179895 5342.0 -1.522247 \n",
"AAACCCAAGAAGCCAC-34 0.105287 17305.0 0.384157 \n",
"\n",
" core_scale_factor ... sex age perturbation \\\n",
"cell_barcode ... \n",
"AAACCCAAGAAATCCA-27 0.813253 ... Female 53 NAF1 \n",
"AAACCCAAGAACTTCC-31 0.844107 ... Female 53 BUB1 \n",
"AAACCCAAGAAGCCAC-34 1.091537 ... Female 53 UBL5 \n",
"\n",
" organism perturbation_type tissue_type ncounts ngenes \\\n",
"cell_barcode \n",
"AAACCCAAGAAATCCA-27 human CRISPR cell_line 11324.0 3332 \n",
"AAACCCAAGAACTTCC-31 human CRISPR cell_line 5257.0 2192 \n",
"AAACCCAAGAAGCCAC-34 human CRISPR cell_line 17135.0 4002 \n",
"\n",
" nperts percent_ribo \n",
"cell_barcode \n",
"AAACCCAAGAAATCCA-27 1 0.225362 \n",
"AAACCCAAGAACTTCC-31 1 0.129732 \n",
"AAACCCAAGAAGCCAC-34 1 0.236825 \n",
"\n",
"[3 rows x 24 columns]\n",
"var head:\n",
" chr start end class strand length in_matrix \\\n",
"gene_name \n",
"LINC01409 chr1 778747 810065 gene_version10 + 31318 True \n",
"LINC01128 chr1 825138 868202 gene_version9 + 43064 True \n",
"NOC2L chr1 944203 959309 gene_version11 - 15106 True \n",
"\n",
" mean std cv fano ensembl_id ncounts \\\n",
"gene_name \n",
"LINC01409 0.137594 0.380048 2.762105 1.049733 ENSG00000237491 42707.0 \n",
"LINC01128 0.256720 0.520162 2.026184 1.053944 ENSG00000228794 79682.0 \n",
"NOC2L 1.975144 1.707837 0.864665 1.476706 ENSG00000188976 613055.0 \n",
"\n",
" ncells \n",
"gene_name \n",
"LINC01409 39082 \n",
"LINC01128 68732 \n",
"NOC2L 248759 \n"
]
}
],
"source": [
"for path in H5AD_FILES:\n",
" summarize_anndata(path)"
]
},
{
"cell_type": "markdown",
"id": "step1",
"metadata": {},
"source": [
"## 2. 对比不同数据集的 `obs` 字段\n",
"\n",
"这一部分会把每个文件里的观测列、候选 perturbation 列和基础统计列统一汇总出来。"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "schema-helpers",
"metadata": {},
"outputs": [],
"source": [
"PERTURBATION_COLUMN_CANDIDATES = [\n",
" \"perturbation\",\n",
" \"gene\",\n",
" \"gene_id\",\n",
" \"gene_transcript\",\n",
" \"guide_id\",\n",
" \"target_gene\",\n",
" \"condition\",\n",
"]\n",
"\n",
"COUNT_COLUMN_CANDIDATES = [\"ncounts\", \"UMI_count\", \"UMI count\", \"read count\"]\n",
"GENE_COUNT_COLUMN_CANDIDATES = [\"ngenes\"]\n",
"\n",
"\n",
"def available_columns(obs_columns: list[str], candidates: list[str]) -> list[str]:\n",
" return [column for column in candidates if column in obs_columns]\n",
"\n",
"\n",
"def matrix_storage_summary(adata) -> dict:\n",
" return {\n",
" \"x_storage\": type(adata.X).__name__,\n",
" \"has_raw\": adata.raw is not None,\n",
" \"raw_shape\": None if adata.raw is None else adata.raw.shape,\n",
" \"layers\": list(adata.layers.keys()),\n",
" \"obsm\": list(adata.obsm.keys()),\n",
" \"varm\": list(adata.varm.keys()),\n",
" \"uns\": list(adata.uns.keys()),\n",
" }\n",
"\n",
"\n",
"def summarize_schema(path: Path) -> dict:\n",
" adata = ad.read_h5ad(path, backed=\"r\")\n",
" try:\n",
" obs_columns = list(adata.obs.columns)\n",
" var_columns = list(adata.var.columns)\n",
" matrix_info = matrix_storage_summary(adata)\n",
" return {\n",
" \"file_name\": path.name,\n",
" \"dataset_name\": path.stem,\n",
" \"n_cells\": adata.n_obs,\n",
" \"n_genes\": adata.n_vars,\n",
" \"obs_columns\": obs_columns,\n",
" \"var_columns\": var_columns,\n",
" \"candidate_perturbation_columns\": available_columns(obs_columns, PERTURBATION_COLUMN_CANDIDATES),\n",
" \"candidate_count_columns\": available_columns(obs_columns, COUNT_COLUMN_CANDIDATES),\n",
" \"candidate_gene_count_columns\": available_columns(obs_columns, GENE_COUNT_COLUMN_CANDIDATES),\n",
" **matrix_info,\n",
" }\n",
" finally:\n",
" if getattr(adata, \"file\", None) is not None:\n",
" adata.file.close()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "schema-summary",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>file_name</th>\n",
" <th>n_cells</th>\n",
" <th>n_genes</th>\n",
" <th>candidate_perturbation_columns</th>\n",
" <th>candidate_count_columns</th>\n",
" <th>candidate_gene_count_columns</th>\n",
" <th>x_storage</th>\n",
" <th>has_raw</th>\n",
" <th>layers</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001.h5ad</td>\n",
" <td>5768</td>\n",
" <td>35635</td>\n",
" <td>[perturbation]</td>\n",
" <td>[ncounts, UMI count, read count]</td>\n",
" <td>[ngenes]</td>\n",
" <td>_CSCDataset</td>\n",
" <td>False</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>AdamsonWeissman2016_GSM2406677_10X005.h5ad</td>\n",
" <td>15006</td>\n",
" <td>32738</td>\n",
" <td>[perturbation]</td>\n",
" <td>[ncounts, UMI count, read count]</td>\n",
" <td>[ngenes]</td>\n",
" <td>_CSCDataset</td>\n",
" <td>False</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>AdamsonWeissman2016_GSM2406681_10X010.h5ad</td>\n",
" <td>65337</td>\n",
" <td>32738</td>\n",
" <td>[perturbation]</td>\n",
" <td>[ncounts, UMI count, read count]</td>\n",
" <td>[ngenes]</td>\n",
" <td>_CSCDataset</td>\n",
" <td>False</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>ReplogleWeissman2022_K562_essential.h5ad</td>\n",
" <td>310385</td>\n",
" <td>8563</td>\n",
" <td>[perturbation, gene, gene_id, gene_transcript,...</td>\n",
" <td>[ncounts, UMI_count]</td>\n",
" <td>[ngenes]</td>\n",
" <td>Dataset</td>\n",
" <td>False</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" file_name n_cells n_genes \\\n",
"0 AdamsonWeissman2016_GSM2406675_10X001.h5ad 5768 35635 \n",
"1 AdamsonWeissman2016_GSM2406677_10X005.h5ad 15006 32738 \n",
"2 AdamsonWeissman2016_GSM2406681_10X010.h5ad 65337 32738 \n",
"3 ReplogleWeissman2022_K562_essential.h5ad 310385 8563 \n",
"\n",
" candidate_perturbation_columns \\\n",
"0 [perturbation] \n",
"1 [perturbation] \n",
"2 [perturbation] \n",
"3 [perturbation, gene, gene_id, gene_transcript,... \n",
"\n",
" candidate_count_columns candidate_gene_count_columns x_storage \\\n",
"0 [ncounts, UMI count, read count] [ngenes] _CSCDataset \n",
"1 [ncounts, UMI count, read count] [ngenes] _CSCDataset \n",
"2 [ncounts, UMI count, read count] [ngenes] _CSCDataset \n",
"3 [ncounts, UMI_count] [ngenes] Dataset \n",
"\n",
" has_raw layers \n",
"0 False [] \n",
"1 False [] \n",
"2 False [] \n",
"3 False [] "
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"schema_summary = pd.DataFrame([summarize_schema(path) for path in H5AD_FILES])\n",
"schema_summary[[\n",
" \"file_name\",\n",
" \"n_cells\",\n",
" \"n_genes\",\n",
" \"candidate_perturbation_columns\",\n",
" \"candidate_count_columns\",\n",
" \"candidate_gene_count_columns\",\n",
" \"x_storage\",\n",
" \"has_raw\",\n",
" \"layers\",\n",
"]]"
]
},
{
"cell_type": "markdown",
"id": "step2",
"metadata": {},
"source": [
"## 3. 统一定位 perturbation 信息与矩阵位置\n",
"\n",
"这里做两个判断：\n",
"\n",
"- 这个数据集主要用哪一列表示 perturbation\n",
"- 表达矩阵主要在 `X`、`raw` 还是 `layers`"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "standardization-helpers",
"metadata": {},
"outputs": [],
"source": [
"CONTROL_PATTERN = re.compile(r\"ctrl|control|neg|non-target|nontarget|ntc|\\*|nan\", re.IGNORECASE)\n",
"\n",
"\n",
"def choose_first_existing(obs_columns: list[str], candidates: list[str]) -> str | None:\n",
" for column in candidates:\n",
" if column in obs_columns:\n",
" return column\n",
" return None\n",
"\n",
"\n",
"def infer_expression_location(adata) -> str:\n",
" if len(adata.layers.keys()) > 0:\n",
" return f\"X + layers={list(adata.layers.keys())}\"\n",
" if adata.raw is not None:\n",
" return \"X + raw\"\n",
" return \"X only\"\n",
"\n",
"\n",
"def infer_single_perturbation(obs_df: pd.DataFrame, perturbation_col: str | None) -> pd.Series:\n",
" if \"nperts\" in obs_df.columns:\n",
" return pd.to_numeric(obs_df[\"nperts\"], errors=\"coerce\").fillna(-1).eq(1)\n",
"\n",
" if perturbation_col is None:\n",
" return pd.Series(False, index=obs_df.index)\n",
"\n",
" text = obs_df[perturbation_col].astype(str)\n",
" delimiters = text.str.contains(r\"[|,+;]\", regex=True)\n",
" looks_control = text.str.contains(CONTROL_PATTERN)\n",
" return (~delimiters) & (~looks_control)\n",
"\n",
"\n",
"def infer_control(obs_df: pd.DataFrame, perturbation_col: str | None) -> pd.Series:\n",
" if perturbation_col is None:\n",
" return pd.Series(False, index=obs_df.index)\n",
" return obs_df[perturbation_col].astype(str).str.contains(CONTROL_PATTERN)\n",
"\n",
"\n",
"def standardize_obs(path: Path) -> pd.DataFrame:\n",
" adata = ad.read_h5ad(path, backed=\"r\")\n",
" try:\n",
" obs = adata.obs.copy()\n",
" obs_columns = list(obs.columns)\n",
"\n",
" perturbation_col = choose_first_existing(obs_columns, [\"perturbation\", \"gene\", \"condition\"])\n",
" gene_col = choose_first_existing(obs_columns, [\"gene\", \"target_gene\", \"perturbation\"])\n",
" gene_id_col = choose_first_existing(obs_columns, [\"gene_id\"])\n",
" guide_col = choose_first_existing(obs_columns, [\"guide_id\"])\n",
" count_col = choose_first_existing(obs_columns, [\"ncounts\", \"UMI_count\", \"UMI count\", \"read count\"])\n",
" ngenes_col = choose_first_existing(obs_columns, [\"ngenes\"])\n",
" perturbation_type_col = choose_first_existing(obs_columns, [\"perturbation_type\"])\n",
" cell_line_col = choose_first_existing(obs_columns, [\"cell_line\"])\n",
" celltype_col = choose_first_existing(obs_columns, [\"celltype\", \"cell_type\"])\n",
" organism_col = choose_first_existing(obs_columns, [\"organism\"])\n",
" disease_col = choose_first_existing(obs_columns, [\"disease\"])\n",
"\n",
" standardized = pd.DataFrame(index=obs.index)\n",
" standardized[\"dataset_name\"] = path.stem\n",
" standardized[\"file_name\"] = path.name\n",
" standardized[\"cell_barcode\"] = obs.index.astype(str)\n",
" standardized[\"perturbation_label\"] = None if perturbation_col is None else obs[perturbation_col].astype(str)\n",
" standardized[\"perturbation_gene\"] = None if gene_col is None else obs[gene_col].astype(str)\n",
" standardized[\"perturbation_gene_id\"] = None if gene_id_col is None else obs[gene_id_col].astype(str)\n",
" standardized[\"guide_id\"] = None if guide_col is None else obs[guide_col].astype(str)\n",
" standardized[\"perturbation_type\"] = None if perturbation_type_col is None else obs[perturbation_type_col].astype(str)\n",
" standardized[\"cell_line\"] = None if cell_line_col is None else obs[cell_line_col].astype(str)\n",
" standardized[\"celltype\"] = None if celltype_col is None else obs[celltype_col].astype(str)\n",
" standardized[\"organism\"] = None if organism_col is None else obs[organism_col].astype(str)\n",
" standardized[\"disease\"] = None if disease_col is None else obs[disease_col].astype(str)\n",
" standardized[\"ncounts\"] = None if count_col is None else pd.to_numeric(obs[count_col], errors=\"coerce\")\n",
" standardized[\"ngenes\"] = None if ngenes_col is None else pd.to_numeric(obs[ngenes_col], errors=\"coerce\")\n",
" standardized[\"nperts\"] = pd.to_numeric(obs[\"nperts\"], errors=\"coerce\") if \"nperts\" in obs.columns else pd.NA\n",
" standardized[\"is_control\"] = infer_control(obs, perturbation_col)\n",
" standardized[\"is_single_perturbation\"] = infer_single_perturbation(obs, perturbation_col)\n",
" standardized[\"expression_location\"] = infer_expression_location(adata)\n",
" standardized[\"source_perturbation_col\"] = perturbation_col\n",
" standardized[\"source_gene_col\"] = gene_col\n",
" standardized[\"source_gene_id_col\"] = gene_id_col\n",
" standardized[\"source_guide_col\"] = guide_col\n",
"\n",
" return standardized.reset_index(drop=True)\n",
" finally:\n",
" if getattr(adata, \"file\", None) is not None:\n",
" adata.file.close()"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "metadata-standardized",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>dataset_name</th>\n",
" <th>file_name</th>\n",
" <th>cell_barcode</th>\n",
" <th>perturbation_label</th>\n",
" <th>perturbation_gene</th>\n",
" <th>perturbation_gene_id</th>\n",
" <th>guide_id</th>\n",
" <th>perturbation_type</th>\n",
" <th>cell_line</th>\n",
" <th>celltype</th>\n",
" <th>...</th>\n",
" <th>ncounts</th>\n",
" <th>ngenes</th>\n",
" <th>nperts</th>\n",
" <th>is_control</th>\n",
" <th>is_single_perturbation</th>\n",
" <th>expression_location</th>\n",
" <th>source_perturbation_col</th>\n",
" <th>source_gene_col</th>\n",
" <th>source_gene_id_col</th>\n",
" <th>source_guide_col</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001</td>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001.h5ad</td>\n",
" <td>AAACATACACCGAT</td>\n",
" <td>CREB1_pDS269</td>\n",
" <td>CREB1_pDS269</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CRISPR</td>\n",
" <td>K562</td>\n",
" <td>lymphoblasts</td>\n",
" <td>...</td>\n",
" <td>8138.0</td>\n",
" <td>2412</td>\n",
" <td>2</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>X only</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001</td>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001.h5ad</td>\n",
" <td>AAACATACAGAGAT</td>\n",
" <td>SNAI1_pDS266</td>\n",
" <td>SNAI1_pDS266</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CRISPR</td>\n",
" <td>K562</td>\n",
" <td>lymphoblasts</td>\n",
" <td>...</td>\n",
" <td>8980.0</td>\n",
" <td>2386</td>\n",
" <td>2</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>X only</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001</td>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001.h5ad</td>\n",
" <td>AAACATACCAGAAA</td>\n",
" <td>62(mod)_pBA581</td>\n",
" <td>62(mod)_pBA581</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CRISPR</td>\n",
" <td>K562</td>\n",
" <td>lymphoblasts</td>\n",
" <td>...</td>\n",
" <td>28610.0</td>\n",
" <td>4404</td>\n",
" <td>2</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>X only</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001</td>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001.h5ad</td>\n",
" <td>AAACATACGTTGAC</td>\n",
" <td>EP300_pDS268</td>\n",
" <td>EP300_pDS268</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CRISPR</td>\n",
" <td>K562</td>\n",
" <td>lymphoblasts</td>\n",
" <td>...</td>\n",
" <td>11346.0</td>\n",
" <td>2815</td>\n",
" <td>2</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>X only</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001</td>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001.h5ad</td>\n",
" <td>AAACATACTGTTCT</td>\n",
" <td>62(mod)_pBA581</td>\n",
" <td>62(mod)_pBA581</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>CRISPR</td>\n",
" <td>K562</td>\n",
" <td>lymphoblasts</td>\n",
" <td>...</td>\n",
" <td>9864.0</td>\n",
" <td>2584</td>\n",
" <td>2</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>X only</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5 rows × 22 columns</p>\n",
"</div>"
],
"text/plain": [
" dataset_name \\\n",
"0 AdamsonWeissman2016_GSM2406675_10X001 \n",
"1 AdamsonWeissman2016_GSM2406675_10X001 \n",
"2 AdamsonWeissman2016_GSM2406675_10X001 \n",
"3 AdamsonWeissman2016_GSM2406675_10X001 \n",
"4 AdamsonWeissman2016_GSM2406675_10X001 \n",
"\n",
" file_name cell_barcode \\\n",
"0 AdamsonWeissman2016_GSM2406675_10X001.h5ad AAACATACACCGAT \n",
"1 AdamsonWeissman2016_GSM2406675_10X001.h5ad AAACATACAGAGAT \n",
"2 AdamsonWeissman2016_GSM2406675_10X001.h5ad AAACATACCAGAAA \n",
"3 AdamsonWeissman2016_GSM2406675_10X001.h5ad AAACATACGTTGAC \n",
"4 AdamsonWeissman2016_GSM2406675_10X001.h5ad AAACATACTGTTCT \n",
"\n",
" perturbation_label perturbation_gene perturbation_gene_id guide_id \\\n",
"0 CREB1_pDS269 CREB1_pDS269 None None \n",
"1 SNAI1_pDS266 SNAI1_pDS266 None None \n",
"2 62(mod)_pBA581 62(mod)_pBA581 None None \n",
"3 EP300_pDS268 EP300_pDS268 None None \n",
"4 62(mod)_pBA581 62(mod)_pBA581 None None \n",
"\n",
" perturbation_type cell_line celltype ... ncounts ngenes nperts \\\n",
"0 CRISPR K562 lymphoblasts ... 8138.0 2412 2 \n",
"1 CRISPR K562 lymphoblasts ... 8980.0 2386 2 \n",
"2 CRISPR K562 lymphoblasts ... 28610.0 4404 2 \n",
"3 CRISPR K562 lymphoblasts ... 11346.0 2815 2 \n",
"4 CRISPR K562 lymphoblasts ... 9864.0 2584 2 \n",
"\n",
" is_control is_single_perturbation expression_location \\\n",
"0 False False X only \n",
"1 False False X only \n",
"2 False False X only \n",
"3 False False X only \n",
"4 False False X only \n",
"\n",
" source_perturbation_col source_gene_col source_gene_id_col source_guide_col \n",
"0 perturbation perturbation None None \n",
"1 perturbation perturbation None None \n",
"2 perturbation perturbation None None \n",
"3 perturbation perturbation None None \n",
"4 perturbation perturbation None None \n",
"\n",
"[5 rows x 22 columns]"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"standardized_metadata = pd.concat([standardize_obs(path) for path in H5AD_FILES], ignore_index=True)\n",
"standardized_metadata.head()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "dataset-level-summary",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>dataset_name</th>\n",
" <th>n_cells</th>\n",
" <th>n_single_perturbation</th>\n",
" <th>n_control</th>\n",
" <th>perturbation_type</th>\n",
" <th>cell_line</th>\n",
" <th>source_perturbation_col</th>\n",
" <th>source_gene_col</th>\n",
" <th>source_guide_col</th>\n",
" <th>expression_location</th>\n",
" <th>single_perturbation_ratio</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>AdamsonWeissman2016_GSM2406675_10X001</td>\n",
" <td>5768</td>\n",
" <td>6</td>\n",
" <td>16</td>\n",
" <td>[CRISPR]</td>\n",
" <td>[K562]</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>X only</td>\n",
" <td>0.001040</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>AdamsonWeissman2016_GSM2406677_10X005</td>\n",
" <td>15006</td>\n",
" <td>13</td>\n",
" <td>3674</td>\n",
" <td>[CRISPR]</td>\n",
" <td>[K562]</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>X only</td>\n",
" <td>0.000866</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>AdamsonWeissman2016_GSM2406681_10X010</td>\n",
" <td>65337</td>\n",
" <td>101</td>\n",
" <td>2714</td>\n",
" <td>[CRISPR]</td>\n",
" <td>[K562]</td>\n",
" <td>perturbation</td>\n",
" <td>perturbation</td>\n",
" <td>None</td>\n",
" <td>X only</td>\n",
" <td>0.001546</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>ReplogleWeissman2022_K562_essential</td>\n",
" <td>310385</td>\n",
" <td>299694</td>\n",
" <td>10816</td>\n",
" <td>[CRISPR]</td>\n",
" <td>[K562]</td>\n",
" <td>perturbation</td>\n",
" <td>gene</td>\n",
" <td>guide_id</td>\n",
" <td>X only</td>\n",
" <td>0.965556</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" dataset_name n_cells n_single_perturbation \\\n",
"0 AdamsonWeissman2016_GSM2406675_10X001 5768 6 \n",
"1 AdamsonWeissman2016_GSM2406677_10X005 15006 13 \n",
"2 AdamsonWeissman2016_GSM2406681_10X010 65337 101 \n",
"3 ReplogleWeissman2022_K562_essential 310385 299694 \n",
"\n",
" n_control perturbation_type cell_line source_perturbation_col \\\n",
"0 16 [CRISPR] [K562] perturbation \n",
"1 3674 [CRISPR] [K562] perturbation \n",
"2 2714 [CRISPR] [K562] perturbation \n",
"3 10816 [CRISPR] [K562] perturbation \n",
"\n",
" source_gene_col source_guide_col expression_location \\\n",
"0 perturbation None X only \n",
"1 perturbation None X only \n",
"2 perturbation None X only \n",
"3 gene guide_id X only \n",
"\n",
" single_perturbation_ratio \n",
"0 0.001040 \n",
"1 0.000866 \n",
"2 0.001546 \n",
"3 0.965556 "
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dataset_level_summary = (\n",
" standardized_metadata.groupby(\"dataset_name\", as_index=False)\n",
" .agg(\n",
" n_cells=(\"cell_barcode\", \"size\"),\n",
" n_single_perturbation=(\"is_single_perturbation\", \"sum\"),\n",
" n_control=(\"is_control\", \"sum\"),\n",
" perturbation_type=(\"perturbation_type\", lambda x: sorted(pd.Series(x).dropna().unique().tolist())),\n",
" cell_line=(\"cell_line\", lambda x: sorted(pd.Series(x).dropna().unique().tolist())),\n",
" source_perturbation_col=(\"source_perturbation_col\", \"first\"),\n",
" source_gene_col=(\"source_gene_col\", \"first\"),\n",
" source_guide_col=(\"source_guide_col\", \"first\"),\n",
" expression_location=(\"expression_location\", \"first\"),\n",
" )\n",
")\n",
"dataset_level_summary[\"single_perturbation_ratio\"] = (\n",
" dataset_level_summary[\"n_single_perturbation\"] / dataset_level_summary[\"n_cells\"]\n",
")\n",
"dataset_level_summary"
]
},
{
"cell_type": "markdown",
"id": "step4",
"metadata": {},
"source": [
"## 4. 导出标准化 metadata\n",
"\n",
"下面会把统一后的细胞级 metadata 和数据集级摘要保存到 `data/processed/scPerturb/`，方便后续模型训练或统计分析直接读取。"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "export-metadata",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Saved cell metadata to: /Users/yurujiang/Desktop/final_thesis/data/processed/scPerturb/cell_metadata_standardized.csv\n",
"Saved dataset summary to: /Users/yurujiang/Desktop/final_thesis/data/processed/scPerturb/dataset_summary.csv\n"
]
}
],
"source": [
"OUTPUT_DIR = PROJECT_ROOT / \"data\" / \"processed\" / \"scPerturb\"\n",
"OUTPUT_DIR.mkdir(parents=True, exist_ok=True)\n",
"\n",
"cell_metadata_path = OUTPUT_DIR / \"cell_metadata_standardized.csv\"\n",
"dataset_summary_path = OUTPUT_DIR / \"dataset_summary.csv\"\n",
"\n",
"standardized_metadata.to_csv(cell_metadata_path, index=False)\n",
"dataset_level_summary.to_csv(dataset_summary_path, index=False)\n",
"\n",
"print(f\"Saved cell metadata to: {cell_metadata_path}\")\n",
"print(f\"Saved dataset summary to: {dataset_summary_path}\")"
]
}
],
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"display_name": "base",
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"name": "python3"
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"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
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|