#!/bin/bash
# 测试 Annotation Skill 与富集分析的集成

set -e

echo "=========================================="
echo "测试 Annotation Skill"
echo "=========================================="

# 1. 准备测试数据
echo "[1/4] 准备测试数据..."
TEST_DIR="/tmp/test_annotation_skill_$(date +%s)"
mkdir -p "$TEST_DIR"

# 使用已有的 Ft.SPL 蛋白序列
PEP_FILE="/home/xia-lab/wutx/00test/bbav20311/assets/examples/test_input/test_final/final/Ft.SPL.final_members.pep.fa"
DE_DIR="/home/xia-lab/wutx/00test/bbav20311/test_rnaseq_de"

echo "  蛋白文件: $PEP_FILE"
echo "  DE结果目录: $DE_DIR"

# 2. 运行技能注释
echo ""
echo "[2/4] 运行技能注释 (API模式)..."
python /home/xia-lab/wutx/00test/bbav20311/skills/annotation/run_api.py \
    --input "$PEP_FILE" \
    --output "$TEST_DIR/annotation" \
    --prefix ftspl \
    --delay 1.0

echo ""
echo "  技能注释完成，输出目录: $TEST_DIR/annotation"
echo "  生成的文件:"
ls -la "$TEST_DIR/annotation/"

# 3. 检查 gene2go.txt 格式
echo ""
echo "[3/4] 检查 gene2go.txt 格式..."
echo "  前10行:"
head -10 "$TEST_DIR/annotation/ftspl.gene2go.txt"

# 4. 运行富集分析（使用技能生成的 gene2go）
echo ""
echo "[4/4] 运行富集分析..."
python /home/xia-lab/wutx/00test/bbav20311/apps/cli/run_rnaseq_enrich.py \
    --input "$DE_DIR/final" \
    --output "$TEST_DIR/enrich" \
    --species ath \
    --gene2go "$TEST_DIR/annotation/ftspl.gene2go.txt" \
    --prefix test

echo ""
echo "  富集分析完成，输出目录: $TEST_DIR/enrich"
echo "  生成的文件:"
find "$TEST_DIR/enrich" -type f | head -20

echo ""
echo "=========================================="
echo "测试完成!"
echo "=========================================="
echo ""
echo "输出位置:"
echo "  技能注释: $TEST_DIR/annotation/"
echo "  富集分析: $TEST_DIR/enrich/"
echo ""
echo "你可以查看:"
echo "  cat $TEST_DIR/annotation/report.md"
echo "  cat $TEST_DIR/enrich/final/test.rnaseq_enrich_report.md"