100 lines
2.9 KiB
Bash
Executable File
100 lines
2.9 KiB
Bash
Executable File
#!/bin/bash
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# 完整集成测试：技能注释 + 富集分析
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set -e
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echo "=========================================="
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echo "集成测试：技能注释 + 富集分析"
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echo "=========================================="
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# 配置
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BASE_DIR="/home/xia-lab/wutx/00test/bbav20311/test_integration"
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OUTPUT_DIR="$BASE_DIR/output"
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ANNOTATION_OUTPUT="$OUTPUT_DIR/annotation"
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ENRICH_OUTPUT="$OUTPUT_DIR/enrich"
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# 清理旧输出
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rm -rf "$OUTPUT_DIR"
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mkdir -p "$ANNOTATION_OUTPUT" "$ENRICH_OUTPUT"
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echo ""
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echo "=========================================="
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echo "第1步：技能注释 (API模式)"
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echo "=========================================="
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echo "输入: $BASE_DIR/annotation_input/proteins.pep.fa"
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echo "输出: $ANNOTATION_OUTPUT"
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echo ""
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python /home/xia-lab/wutx/00test/bbav20311/skills/annotation/run_api.py \
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--input "$BASE_DIR/annotation_input/proteins.pep.fa" \
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--output "$ANNOTATION_OUTPUT" \
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--prefix ftspl \
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--delay 1.0
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echo ""
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echo "✅ 技能注释完成"
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echo ""
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echo "生成的文件:"
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ls -lh "$ANNOTATION_OUTPUT/"
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echo ""
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echo "gene2go.txt 前10行:"
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head -10 "$ANNOTATION_OUTPUT/ftspl.gene2go.txt"
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echo ""
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echo "=========================================="
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echo "第2步：富集分析 (使用技能生成的gene2go)"
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echo "=========================================="
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echo "输入 DE genes: $BASE_DIR/de_input/"
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echo "输入 gene2go: $ANNOTATION_OUTPUT/ftspl.gene2go.txt"
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echo "输出: $ENRICH_OUTPUT"
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echo ""
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python /home/xia-lab/wutx/00test/bbav20311/apps/cli/run_rnaseq_enrich.py \
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--input "$BASE_DIR/de_input" \
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--output "$ENRICH_OUTPUT" \
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--species ath \
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--gene2go "$ANNOTATION_OUTPUT/ftspl.gene2go.txt" \
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--prefix ftspl_enrich
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echo ""
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echo "✅ 富集分析完成"
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echo ""
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echo "生成的文件:"
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find "$ENRICH_OUTPUT" -type f | sort
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echo ""
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echo "=========================================="
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echo "测试结果汇总"
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echo "=========================================="
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echo ""
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echo "1. 技能注释输出:"
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echo " 位置: $ANNOTATION_OUTPUT"
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echo " 文件数: $(find "$ANNOTATION_OUTPUT" -type f | wc -l)"
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echo ""
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echo "2. 富集分析输出:"
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echo " 位置: $ENRICH_OUTPUT"
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echo " 文件数: $(find "$ENRICH_OUTPUT" -type f | wc -l)"
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echo ""
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echo "3. 关键文件:"
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echo " - gene2go: $ANNOTATION_OUTPUT/ftspl.gene2go.txt"
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echo " - GO富集: $ENRICH_OUTPUT/final/ftspl_enrich.GO_enrich.txt"
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echo " - GO图表: $ENRICH_OUTPUT/final/ftspl_enrich_GO_enrich.png"
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echo ""
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echo "=========================================="
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echo "查看结果命令:"
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echo "=========================================="
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echo ""
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echo "# 技能注释报告"
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echo "cat $ANNOTATION_OUTPUT/report.md"
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echo ""
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echo "# gene2go 内容"
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echo "cat $ANNOTATION_OUTPUT/ftspl.gene2go.txt"
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echo ""
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echo "# 富集分析报告"
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echo "cat $ENRICH_OUTPUT/final/ftspl_enrich.rnaseq_enrich_report.md"
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echo ""
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echo "# GO富集结果"
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echo "cat $ENRICH_OUTPUT/final/ftspl_enrich.GO_enrich.txt"
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echo ""
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