undisplayed_scaffold_pathwayTools合并

Submitted by admin on Sun, 10/26/2025 - 14:07

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如何修改您的 genetic-elements.dat 文件 PS：最安全、最规范的做法： 保留 CIRCULAR? N 这一行。

要显示 Chr01 到 Chr06，并隐藏 Chr07，您需要做如下修改：

为您希望显示的染色体（Chr01 到 Chr06）添加 TYPE :CHRSM。
为您希望隐藏的染色体（Chr07）添加 TYPE :CONTIG。

修改后的 genetic-elements.dat 示例：

// 这是Chr01，我们希望显示它
ID GEN-EL291832
NAME Chr01
TYPE :CHRSM
ANNOT-FILE Chr01.pf
SEQ-FILE Chr01.fna
CODON-TABLE 1
//
ID GEN-EL291833
NAME Chr02
TYPE :CHRSM
ANNOT-FILE Chr02.pf
SEQ-FILE Chr02.fna
CODON-TABLE 1
//
ID GEN-EL291834
NAME Chr03
TYPE :CHRSM
ANNOT-FILE Chr03.pf
SEQ-FILE Chr03.fna
CODON-TABLE 1
//
ID GEN-EL291835
NAME Chr04
TYPE :CHRSM
ANNOT-FILE Chr04.pf
SEQ-FILE Chr04.fna
CODON-TABLE 1
//
ID GEN-EL291836
NAME Chr05
TYPE :CHRSM
ANNOT-FILE Chr05.pf
SEQ-FILE Chr05.fna
CODON-TABLE 1
//
ID GEN-EL291837
NAME Chr06
TYPE :CHRSM
ANNOT-FILE Chr06.pf
SEQ-FILE Chr06.fna
CODON-TABLE 1
//
// 这是Chr07，我们希望隐藏它
ID GEN-EL291838
NAME Chr07
TYPE :CONTIG
ANNOT-FILE Chr07.pf
SEQ-FILE Chr07.fna
CODON-TABLE 1
//

总结

您只需要在 genetic-elements.dat 文件的每个条目中，根据需要添加 TYPE :CHRSM 或 TYPE :CONTIG 即可控制其在Pathway Tools网站主页上的显示状态。

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是的，建议在注释前就合并！

推荐的工作流程

在运行 Pathologic 注释之前：

bash

# 1. 准备主要染色体文件（保持独立）
Chr01.pf
Chr01.fna
Chr02.pf
Chr02.fna
...

# 2. 合并所有小scaffolds（注释前就合并）
cat scaffold_*.pf > undisplayed_scaffolds.pf
cat scaffold_*.fna > undisplayed_scaffolds.fna

# 3. 删除原始的小scaffold文件（可选）
rm scaffold_*.pf scaffold_*.fna

不会影响 Pathologic 注释！

合并文件完全不影响注释质量，因为：

✅ Pathologic 只关心：

基因的坐标信息
基因的序列
功能注释信息

✅ 不关心：

文件是分开的还是合并的
Contig/scaffold 的数量
文件的命名

genetic-elements.dat 的两种配置方式

方式1：不定义 undisplayed scaffolds（推荐）

dat

# genetic-elements.dat
ID GEN-EL001
NAME Chr01
ANNOT-FILE Chr01.pf
SEQ-FILE Chr01.fna
CODON-TABLE 1
//

ID GEN-EL002
NAME Chr02
ANNOT-FILE Chr02.pf
SEQ-FILE Chr02.fna
CODON-TABLE 1
//

# 不要为 undisplayed_scaffolds.pf 创建条目
# PathwayTools 会自动把它们归入 "Undisplayed Contigs/Replicons"

关键： 把 undisplayed_scaffolds.pf 和 undisplayed_scaffolds.fna 放在输入目录中，但不在 genetic-elements.dat 中定义。

方式2：明确定义为特殊类型

dat

# 前面的主染色体定义...

# 最后添加
ID GEN-UNDISPLAYED
NAME Undisplayed_Scaffolds
ANNOT-FILE undisplayed_scaffolds.pf
SEQ-FILE undisplayed_scaffolds.fna
CODON-TABLE 1
TYPE :CONTIG
//

完整的操作步骤

bash

# 1. 进入你的数据目录
cd /path/to/your/organism/input/

# 2. 合并小scaffolds的pf文件
cat scaffold_205.pf scaffold_275.pf scaffold_316.pf ... > undisplayed_scaffolds.pf

# 3. 合并小scaffolds的fna文件
cat scaffold_205.fna scaffold_275.fna scaffold_316.fna ... > undisplayed_scaffolds.fna

# 4. 编辑 genetic-elements.dat（只定义主染色体）
vi genetic-elements.dat

# 5. 运行 Pathologic 注释
pathologic -lisp your_organism_id
```

### .pf 文件格式不会被破坏

合并后的文件格式示例：
```
; 来自 scaffold_205
ID GENE001
NAME gene1
STARTBASE 100
ENDBASE 500
FUNCTION hypothetical protein
//

; 来自 scaffold_275
ID GENE002
NAME gene2
STARTBASE 200
ENDBASE 800
FUNCTION kinase
//

每个基因条目仍然独立，// 分隔符保持清晰，完全不影响解析。

总结

时机
操作
影响注释？

注释前合并
✅ 推荐
❌ 不影响

注释后合并
⚠️ 需要重新运行
❌ 不影响

不合并
可以但复杂
❌ 不影响

最佳实践：注释前就合并好，genetic-elements.dat 中不定义它们，PathwayTools 会自动归类为 "Undisplayed Contigs/Replicons"。

Focusing on User Needs

I've been analyzing the user's request, specifically their need to hide specific scaffolds from the Pathway Tools homepage. The goal is clear: to customize the display. I'm now exploring the implementation details, like identifying the existing mechanism to filter the view, and how to apply this to particular replicon IDs. I'm thinking about the most user-friendly way to achieve this.

Exploring Configuration Options

I'm now investigating the potential for hiding specific scaffolds within the genetic-elements.dat file. The image suggests a default filtering mechanism may exist. I'm looking into how to modify the genetic-elements.dat file to exclude "Chr07" as requested, while considering any potential side effects. I'm also exploring alternative configuration files.

Identifying Hiding Mechanisms

I'm now investigating how the "Unplayed Contigs/Replicons" are managed. The image suggests a filtering system is in place, linked to these "unplayed" categories. I suspect there's a configuration option that controls what constitutes "unplayed," and I'm looking for how to modify this. The focus is on finding an approach that doesn't involve manually editing the genetic-elements.dat file for each scaffold.

Following Key Leads

I've hit a snag. The official source mentions a crucial "Sample PathoLogic genetic- elements.dat file", a really key piece of data. But frustratingly, I can't click on the link to access it. This feels like a definite setback, and I need to find another way to get that file.

Investigating Data Structures

I'm now zeroing in on the file's structure. My breakthrough came with the AuReMe/mpwt GitHub repository. It clearly defines the genetic-elements.dat file and highlights the crucial TYPE field. This contrasts with the user's data, which lacks this critical piece. The summary of "Unplayed Contigs/Replicons" further solidifies my hypothesis that replicons are classified, which directly links to the TYPE field. I need to figure out how to assign these types.

Defining the Data Change

I've identified the solution: modifying the genetic-elements.dat file. By adding the :CONTIG type to the GEN-EL291838 entry (corresponding to Chr07), I can successfully hide it from the homepage. The current file entry lacks a type definition, thus PathoLogic defaults it to a chromosome. My focus is now on the correct file syntax for the update.

Refining Data Formatting

I'm now zeroing in on the best formatting. I've been working on how to modify the genetic elements dat file to add the :CONTIG type to the entry for GEN-EL291838 to hide it from the homepage. I'm focusing on the precise syntax, and ensuring the other chromosomes are correctly typed as chromosomes.

Defining the Implementation

I'm now formulating a precise solution. The user needs to edit the genetic-elements.dat file, specifying :CONTIG type for the entry to be hidden. I'll need to provide clear examples, ensuring the other chromosomes are marked as :CHRSM for display. I must explicitly state that the user needs to re-run PathoLogic for the changes to take effect.

Defining Implementation Details

Now, I'm at the point of finalizing the implementation steps. The user needs to edit their genetic-elements.dat file, adding the :CONTIG type to the GEN-EL291838 entry to hide it, and :CHRSM to the others to ensure their visibility. Clear examples will be provided, and I will stress the need to re-run PathoLogic after the changes are made.

根据您提供的图片和 genetic-elements.dat 文件内容，您猜对了，这个设置正是在 genetic-elements.dat 文件中控制的。

您希望将 "Chr07" 这样的scaffold在主页上隐藏掉，并归入到您图片中红色方框所示的 "Unplayed Contigs/Replicons" 类别中。

这是通过在 genetic-elements.dat 文件中为每个条目添加一个 TYPE 字段来实现的。

TYPE :CHRSM：指定该序列为染色体 (chromosome)，会在主页上明确列出（如您图中的 CM017615.1 等）。
TYPE :CONTIG：指定该序列为普通重叠群 (contig)，这些序列会被归类到 "Unplayed Contigs/Replicons" 中，不会在主页上单独展示。
TYPE :PLASMID：指定该序列为质粒 (plasmid)。

如何修改您的 genetic-elements.dat 文件

要显示 Chr01 到 Chr06，并隐藏 Chr07，您需要做如下修改：

为您希望显示的染色体（Chr01 到 Chr06）添加 TYPE :CHRSM。
为您希望隐藏的染色体（Chr07）添加 TYPE :CONTIG。

修改后的 genetic-elements.dat 示例：

总结

您只需要在 genetic-elements.dat 文件的每个条目中，根据需要添加 TYPE :CHRSM 或 TYPE :CONTIG 即可控制其在Pathway Tools网站主页上的显示状态。

修改此文件后，您需要重新运行PathoLogic来构建或更新您的PGDB，这些更改才能在生成的网站上生效。

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undisplayed_scaffold_pathwayTools合并