#!/bin/bash
# 完整集成测试：技能注释 + 富集分析

set -e

echo "=========================================="
echo "集成测试：技能注释 + 富集分析"
echo "=========================================="

# 配置
BASE_DIR="/home/xia-lab/wutx/00test/bbav20311/test_integration"
OUTPUT_DIR="$BASE_DIR/output"
ANNOTATION_OUTPUT="$OUTPUT_DIR/annotation"
ENRICH_OUTPUT="$OUTPUT_DIR/enrich"

# 清理旧输出
rm -rf "$OUTPUT_DIR"
mkdir -p "$ANNOTATION_OUTPUT" "$ENRICH_OUTPUT"

echo ""
echo "=========================================="
echo "第1步：技能注释 (API模式)"
echo "=========================================="
echo "输入: $BASE_DIR/annotation_input/proteins.pep.fa"
echo "输出: $ANNOTATION_OUTPUT"
echo ""

python /home/xia-lab/wutx/00test/bbav20311/skills/annotation/run_api.py \
    --input "$BASE_DIR/annotation_input/proteins.pep.fa" \
    --output "$ANNOTATION_OUTPUT" \
    --prefix ftspl \
    --delay 1.0

echo ""
echo "✅ 技能注释完成"
echo ""
echo "生成的文件:"
ls -lh "$ANNOTATION_OUTPUT/"

echo ""
echo "gene2go.txt 前10行:"
head -10 "$ANNOTATION_OUTPUT/ftspl.gene2go.txt"

echo ""
echo "=========================================="
echo "第2步：富集分析 (使用技能生成的gene2go)"
echo "=========================================="
echo "输入 DE genes: $BASE_DIR/de_input/"
echo "输入 gene2go: $ANNOTATION_OUTPUT/ftspl.gene2go.txt"
echo "输出: $ENRICH_OUTPUT"
echo ""

python /home/xia-lab/wutx/00test/bbav20311/apps/cli/run_rnaseq_enrich.py \
    --input "$BASE_DIR/de_input" \
    --output "$ENRICH_OUTPUT" \
    --species ath \
    --gene2go "$ANNOTATION_OUTPUT/ftspl.gene2go.txt" \
    --prefix ftspl_enrich

echo ""
echo "✅ 富集分析完成"
echo ""
echo "生成的文件:"
find "$ENRICH_OUTPUT" -type f | sort

echo ""
echo "=========================================="
echo "测试结果汇总"
echo "=========================================="
echo ""
echo "1. 技能注释输出:"
echo "   位置: $ANNOTATION_OUTPUT"
echo "   文件数: $(find "$ANNOTATION_OUTPUT" -type f | wc -l)"
echo ""
echo "2. 富集分析输出:"
echo "   位置: $ENRICH_OUTPUT"
echo "   文件数: $(find "$ENRICH_OUTPUT" -type f | wc -l)"
echo ""
echo "3. 关键文件:"
echo "   - gene2go: $ANNOTATION_OUTPUT/ftspl.gene2go.txt"
echo "   - GO富集: $ENRICH_OUTPUT/final/ftspl_enrich.GO_enrich.txt"
echo "   - GO图表: $ENRICH_OUTPUT/final/ftspl_enrich_GO_enrich.png"
echo ""
echo "=========================================="
echo "查看结果命令:"
echo "=========================================="
echo ""
echo "# 技能注释报告"
echo "cat $ANNOTATION_OUTPUT/report.md"
echo ""
echo "# gene2go 内容"
echo "cat $ANNOTATION_OUTPUT/ftspl.gene2go.txt"
echo ""
echo "# 富集分析报告"
echo "cat $ENRICH_OUTPUT/final/ftspl_enrich.rnaseq_enrich_report.md"
echo ""
echo "# GO富集结果"
echo "cat $ENRICH_OUTPUT/final/ftspl_enrich.GO_enrich.txt"
echo ""