146 lines
3.6 KiB
Markdown
Executable File
146 lines
3.6 KiB
Markdown
Executable File
# 番茄P450补充材料手动下载指南
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## 快速下载链接
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### Additional File 1 (关键文件 - 基因列表和分组)
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**直接下载链接**:
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```
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https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-019-5483-x/MediaObjects/12864_2019_5483_MOESM1_ESM.xlsx
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```
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**文件内容**:
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- 233个P450基因列表
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- 系统发育分组（clan/family）
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- 基因ID和名称对应
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---
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## 手动下载步骤
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### 方法1: 直接下载（推荐）
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1. **复制上面的链接**
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2. **粘贴到浏览器地址栏**
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3. **文件会自动下载**
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### 方法2: 从BMC官网下载
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1. 访问: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5483-x
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2. 向下滚动到 "Supplementary information" 部分
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3. 点击 "Additional file 1" 下载
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### 方法3: 使用wget/curl
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```bash
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# 使用wget
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wget "https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-019-5483-x/MediaObjects/12864_2019_5483_MOESM1_ESM.xlsx" \
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-O 12864_2019_5483_MOESM1_ESM.xlsx
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# 或使用curl
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curl -L "https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-019-5483-x/MediaObjects/12864_2019_5483_MOESM1_ESM.xlsx" \
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-o 12864_2019_5483_MOESM1_ESM.xlsx
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```
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---
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## 文件解析
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### 下载后验证
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```python
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import pandas as pd
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# 读取Excel文件
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df = pd.read_excel("12864_2019_5483_MOESM1_ESM.xlsx")
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# 查看前几行
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print(df.head())
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# 查看列名
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print(df.columns)
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# 统计分组信息
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print(df['Clan'].value_counts())
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print(df['Family'].value_counts())
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```
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### 预期数据结构
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| 列名 | 说明 |
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|:---|:---|
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| Gene_ID | 基因ID |
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| Gene_Name | 基因名称 (如 SlCYP71A1) |
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| Clan | 所属clan (如 clan71) |
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| Family | 所属family (如 CYP71) |
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| ... | 其他信息 |
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---
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## 完整补充材料清单
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| 文件名 | 内容 | 重要性 |
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|:---|:---|:---|
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| 12864_2019_5483_MOESM1_ESM.xlsx | **基因列表和系统发育分组** | ⭐⭐⭐ 关键 |
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| 12864_2019_5483_MOESM2_ESM.xlsx | 引物序列 | ⭐ 次要 |
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| 12864_2019_5483_MOESM3_ESM.tif | 系统发育树 (Figure 2) | ⭐⭐⭐ 关键 |
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| 12864_2019_5483_MOESM4_ESM.xlsx | 内含子分析 | ⭐⭐ 重要 |
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| 12864_2019_5483_MOESM5_ESM.xlsx | 启动子分析 | ⭐⭐ 重要 |
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| 12864_2019_5483_MOESM6_ESM.xlsx | 组织特异性表达 | ⭐⭐ 重要 |
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| 12864_2019_5483_MOESM7_ESM.docx | 比较分析 | ⭐ 次要 |
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---
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## 下载后操作
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### 1. 放置到正确目录
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```bash
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# 创建目录
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mkdir -p /home/xia-lab/gene-family-mas-v2/paper/ceshi/番茄P450_supplementary/
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# 移动文件
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mv 12864_2019_5483_MOESM1_ESM.xlsx \
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/home/xia-lab/gene-family-mas-v2/paper/ceshi/番茄P450_supplementary/
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```
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### 2. 验证提取
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```python
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# 运行v3提取脚本，现在应该能获取完整分组
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python extract_phylogeny_v3.py \
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"/home/xia-lab/gene-family-mas-v2/paper/ceshi/番茄p450基因家族BMCgenomics2020.pdf" \
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--supplementary "/home/xia-lab/gene-family-mas-v2/paper/ceshi/番茄P450_supplementary/12864_2019_5483_MOESM1_ESM.xlsx"
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```
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---
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## 注意事项
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1. **文件大小**: MOESM1_ESM.xlsx 约 200-500 KB
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2. **下载时间**: 通常几秒钟
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3. **网络要求**: 需要访问Springer/BMC网站
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4. **权限**: 无需登录，开放获取
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---
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## 自动化方案（未来）
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一旦手动下载验证成功，可以实现：
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```python
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def auto_download_supplementary(doi: str) -> Path:
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"""自动下载补充材料"""
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base_url = "https://static-content.springer.com/esm/"
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encoded_doi = quote(doi, safe='')
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file_url = f"{base_url}art%3A{encoded_doi}/MediaObjects/{pmcid}_MOESM1_ESM.xlsx"
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response = requests.get(file_url)
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# ...保存并返回路径
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```
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---
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*创建时间: 2026-03-30*
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*目标: 获取番茄P450完整系统发育分组数据*
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