8e0deb1691
- 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>
81 lines
2.3 KiB
Markdown
81 lines
2.3 KiB
Markdown
# CRISPR-Cas Analysis Module
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This module provides tools for detecting and analyzing CRISPR-Cas systems in bacterial genomes using CRISPRCasFinder and MacSyFinder.
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## Installation & Setup
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This directory is a standalone `pixi` project.
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1. **Enter the directory**:
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```bash
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cd tools/crispr_cas_analysis
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```
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2. **Install dependencies**:
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```bash
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pixi install
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```
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3. **Install CASFinder Definitions**:
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This step downloads the required CASFinder model definitions.
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```bash
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pixi run install-casfinder
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```
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## Usage
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### Environment
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To run commands, you can either prepend `pixi run` or enter the shell:
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```bash
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pixi shell
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```
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### Running Detection
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Use the provided `CRISPRCasFinder.pl` script to analyze a genome assembly (FASTA format).
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**Example Command (running from `tools/crispr_cas_analysis` directory)**:
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```bash
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# 1. Clean up previous results if they exist
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rm -rf tests/test_output
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# 先创建输出目录（如果不存在）
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mkdir -p ./tests/test_output
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# 进入输出目录
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cd ./tests/test_output
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# 从这里运行命令，调整相关路径
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pixi run perl ../../src/CRISPRCasFinder.pl \
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-in ../20141126CLLT035_contig341.fna \
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-out . \
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-so ../../src/sel392v2.so \
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-cas -q -log
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# # 2. Run detection using relative paths
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pixi run perl src/CRISPRCasFinder.pl \
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-in ./tests/20141126CLLT035_contig341.fna \
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-q -cas -log -html -ccvRep \
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-cpuMacSyFinder 20 \
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-cluster 20000 \
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-getSummaryCasfinder \
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-so /home/gzy/Bt_Project/software/sel392v2.so \
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-gffAnnot /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.gff \
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-proteome /home/gzy/Bt_Project/1_sequencing_genome_annotation/20120412LHLT139/20120412LHLT139.faa
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-out ./tests/test_output \
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-so ./src/sel392v2.so
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```
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### Output Explanation
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The output directory (`tests/test_output`) will contain several key files:
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* `CRISPR-Cas_summary.tsv`: Summary of detected CRISPR arrays and Cas systems.
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* `Cas_REPORT.tsv`: Detailed report of detected Cas proteins.
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* `Crisprs_REPORT.tsv`: Detailed report of detected CRISPR arrays.
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* `GFF/`: Annotations of the findings.
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* `Visualization/`: HTML visualization of the results.
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## Directory Structure
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* `src/`: Source code and scripts (CRISPRCasFinder.pl, etc.).
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* `scripts/`: Wrapper scripts for the pipeline.
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* `tests/`: Test data.
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