69 lines
2.0 KiB
Bash
Executable File
69 lines
2.0 KiB
Bash
Executable File
#!/bin/bash
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# 测试 Annotation Skill 与富集分析的集成
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set -e
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echo "=========================================="
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echo "测试 Annotation Skill"
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echo "=========================================="
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# 1. 准备测试数据
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echo "[1/4] 准备测试数据..."
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TEST_DIR="/tmp/test_annotation_skill_$(date +%s)"
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mkdir -p "$TEST_DIR"
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# 使用已有的 Ft.SPL 蛋白序列
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PEP_FILE="/home/xia-lab/wutx/00test/bbav20311/assets/examples/test_input/test_final/final/Ft.SPL.final_members.pep.fa"
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DE_DIR="/home/xia-lab/wutx/00test/bbav20311/test_rnaseq_de"
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echo " 蛋白文件: $PEP_FILE"
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echo " DE结果目录: $DE_DIR"
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# 2. 运行技能注释
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echo ""
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echo "[2/4] 运行技能注释 (API模式)..."
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python /home/xia-lab/wutx/00test/bbav20311/skills/annotation/run_api.py \
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--input "$PEP_FILE" \
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--output "$TEST_DIR/annotation" \
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--prefix ftspl \
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--delay 1.0
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echo ""
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echo " 技能注释完成，输出目录: $TEST_DIR/annotation"
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echo " 生成的文件:"
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ls -la "$TEST_DIR/annotation/"
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# 3. 检查 gene2go.txt 格式
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echo ""
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echo "[3/4] 检查 gene2go.txt 格式..."
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echo " 前10行:"
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head -10 "$TEST_DIR/annotation/ftspl.gene2go.txt"
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# 4. 运行富集分析（使用技能生成的 gene2go）
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echo ""
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echo "[4/4] 运行富集分析..."
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python /home/xia-lab/wutx/00test/bbav20311/apps/cli/run_rnaseq_enrich.py \
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--input "$DE_DIR/final" \
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--output "$TEST_DIR/enrich" \
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--species ath \
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--gene2go "$TEST_DIR/annotation/ftspl.gene2go.txt" \
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--prefix test
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echo ""
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echo " 富集分析完成，输出目录: $TEST_DIR/enrich"
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echo " 生成的文件:"
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find "$TEST_DIR/enrich" -type f | head -20
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echo ""
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echo "=========================================="
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echo "测试完成!"
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echo "=========================================="
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echo ""
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echo "输出位置:"
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echo " 技能注释: $TEST_DIR/annotation/"
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echo " 富集分析: $TEST_DIR/enrich/"
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echo ""
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echo "你可以查看:"
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echo " cat $TEST_DIR/annotation/report.md"
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echo " cat $TEST_DIR/enrich/final/test.rnaseq_enrich_report.md"
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