# 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.