feat: add base_prokka tool and CRISPR-Cas analysis source code

- Add base_prokka genome annotation tool with pixi config
- Add CRISPR-Cas analysis src (CRISPRCasFinder.pl, environment config)
- Add test data and documentation

Co-Authored-By: Claude <noreply@anthropic.com>

tools/crispr_cas_analysis/README.md

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+# CRISPR-Cas Analysis Module
+
+This module provides tools for detecting and analyzing CRISPR-Cas systems in bacterial genomes using CRISPRCasFinder and MacSyFinder.
+
+## Installation & Setup
+
+This directory is a standalone `pixi` project.
+
+1.  **Enter the directory**:
+    ```bash
+    cd tools/crispr_cas_analysis
+    ```
+
+2.  **Install dependencies**:
+    ```bash
+    pixi install
+    ```
+
+3.  **Install CASFinder Definitions**:
+    This step downloads the required CASFinder model definitions.
+    ```bash
+    pixi run install-casfinder
+    ```
+
+## Usage
+
+### Environment
+To run commands, you can either prepend `pixi run` or enter the shell:
+
+```bash
+pixi shell
+```
+
+### Running Detection
+Use the provided `CRISPRCasFinder.pl` script to analyze a genome assembly (FASTA format).
+
+**Example Command (running from `tools/crispr_cas_analysis` directory)**:
+
+```bash
+# 1. Clean up previous results if they exist
+rm -rf tests/test_output
+# 先创建输出目录（如果不存在）
+mkdir -p ./tests/test_output
+
+# 进入输出目录
+cd ./tests/test_output
+
+# 从这里运行命令，调整相关路径
+pixi run perl ../../src/CRISPRCasFinder.pl \
+-in ../20141126CLLT035_contig341.fna \
+-out . \
+-so ../../src/sel392v2.so \
+-cas -q -log
+
+# # 2. Run detection using relative paths
+pixi run perl src/CRISPRCasFinder.pl \
+  -in ./tests/20141126CLLT035_contig341.fna \
+  -q -cas -log -html -ccvRep \
+  -cpuMacSyFinder 20   \
+  -cluster 20000 \
+  -getSummaryCasfinder \
+  -so /home/gzy/Bt_Project/software/sel392v2.so \
+  -gffAnnot /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.gff \
+  -proteome /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.faa
+  -out ./tests/test_output \
+  -so ./src/sel392v2.so
+```
+
+### Output Explanation
+The output directory (`tests/test_output`) will contain several key files:
+*   `CRISPR-Cas_summary.tsv`: Summary of detected CRISPR arrays and Cas systems.
+*   `Cas_REPORT.tsv`: Detailed report of detected Cas proteins.
+*   `Crisprs_REPORT.tsv`: Detailed report of detected CRISPR arrays.
+*   `GFF/`: Annotations of the findings.
+*   `Visualization/`: HTML visualization of the results.
+
+## Directory Structure
+*   `src/`: Source code and scripts (CRISPRCasFinder.pl, etc.).
+*   `scripts/`: Wrapper scripts for the pipeline.
+*   `tests/`: Test data.

tools/crispr_cas_analysis/result.json

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+{

tools/crispr_cas_analysis/src/02_crispr_cas_completeness.md

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+# 模块 2：CRISPR/Cas 完整性压分（模板）
+
+> 目标：对每个基因组评估 CRISPR/Cas 系统状态，并映射为：  
+> **不存在（0） > 不完整（1） > 完整（2）**，且 **越完整越压分**（负向、单调）。
+
+---
+
+## 1) Conda 环境
+
+- 环境名：`crisprcasfinder`
+- 说明：用于运行 CRISPRCasFinders 检测工具
+- 激活：
+```bash
+conda env create -f ccf.environment.yml -n crisprcasfinder
+conda activate crisprcasfinder
+conda install -c bioconda macsyfinder=2.1.2
+macsydata install -u CASFinder==3.1.0
+```
+
+---
+
+## 2) 启动命令
+
+### 2.1 单基因组运行（示例模板：以“检测 + 完整性判定”两步为例）
+```bash
+# Step 1) 运行crisprcasfinder
+perl ./script/CRISPRCasFinder.pl \
+  -in /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.fna \
+  -q -cas -log -html -ccvRep \ # 参数保持默认
+  -cpuMacSyFinder 20   \
+  -cluster 20000 \
+  -getSummaryCasfinder \
+  -so /home/gzy/Bt_Project/software/sel392v2.so \
+  -gffAnnot /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.gff \
+  -proteome /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.faa
+
+# Step 2) 将检测结果归类为 0/1/2（不存在/不完整/完整）
+python crispr_cas_stats.py \
+  --input <OUTDIR>/CRISPR-Cas_summary.tsv \
+  --output <OUTDIR>/CRISPR-Cas_statistics.tsv
+```
+
+
+---
+
+## 3) 参数说明（阈值含义 + 默认值）
+
+| 参数 | 含义 | 默认值 |
+|---|---|---|
+| `-in` | 基因组fna文件 |
+| `-cpuMacSyFinder` | 线程数 | 1 |
+| `-cluster` | 距离阈值 | 20000 |
+| `-getSummaryCasfinder` | |
+| `-so` | | ./sel392v2.so |
+| `-gffAnnot` | 基因组gff文件 | 来自prokka软件注释的gff文件 |
+| `-proteome` | 基因组faa文件 | 来自prokka软件注释的faa文件 |
+
+---
+
+## 4) 输出结果文件（结构与解析）
+
+### 4.1 CRISPRCasFinder输出目录结构
+```
+OUTDIR/
+  LOGs/
+  TSV/
+    CRISPR-Cas_summary.tsv
+    CRISPR-Cas_clusters.tsv
+    Crisprs_REPORT.tsv
+    Cas_REPORT.tsv
+  Visualization/
+    index.html
+```
+
+### 4.2 crispr_cas_stats.py结果文件结构
+
+| 字段 | 类型 | 说明 |
+|---|---|---|
+| `state` | int | 0: 不存在 CRISPR/Cas系统; 1: CRISPR/Cas系统存在，但不完整; 2: CRISPR/Cas系统存在且完整 |
+| `typess` | string | 推断系统类型（I/II/III/V/…） |
+
+---
+
+
+

tools/crispr_cas_analysis/src/ccf.environment.yml

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+name: crisprcasfinder
+channels:
+- conda-forge
+- bioconda
+- defaults
+dependencies:
+- python >=3.10
+- wget
+- curl
+- git
+- java-jdk
+- parallel
+- perl-app-cpanminus
+- hmmer
+- emboss
+- blast
+- perl-bioperl-core
+- perl-xml-simple
+- perl-digest-md5
+- vmatch
+- muscle
+- prodigal
+- mamba
+- macsyfinder=2.0
+prefix: crisprcasfinder

tools/crispr_cas_analysis/tests/20141126CLLT035_contig341.fna

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+>20141126CLLT035_contig341
+AGAAGGATTTTAAAACCGTAAGACACTTAGAGAGGGGAAACAACTATGTCACTTTTACAG
+CAACATTTTGAAGAAAGAAGAGAATACATTTTCAATCGTCTTAAACAACCAGAATACATG
+GAAAGAAGCATAGAAAAAGTTCGCCAAGCTCAAAAAGAGATCAAAAATACAGTGCGAACG
+ATTAAAGATTTGTTACTCTTAGACAAAACCACTGATCCTTGCCTTTAATTTATTCACTAA
+TATTACACTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTGTTTTTATCATGATGTTTAAT
+GCAAAAGAGAAAATCCTCATGGATTCTTATAAGAAAAAGCGTAGATCACAAACAGAACTT
+CATTATGATGTTGCTGACAAAGAAGGGTTTGACAAAGCGTTTTATGAAGCGCGTATTGAT
+TCATTACGAAATGACATTCGTGTAATATCTTTCAAAAAGCTATGTGAAAATGAACCCGCA
+CCAGAAGACTTAGAACTATTCAAACAACGCTATGAAACAATTGTTTTACCAAAAATACAA
+GAAATTGTTTCCCTAATTGAACCAAGTTTAATAGATATAGACGTATTTTTAAATCCAGTA
+ATCCAATATGGTGTAGGAGAAATTACTTTAGATGAAATGATTCAAAAACTACACAAAAAC
+CTTTCTCTATTTCACGAATTATCAAAGGT