123 lines
4.3 KiB
Bash
Executable File
123 lines
4.3 KiB
Bash
Executable File
#!/bin/bash
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# KaKs 手动测试脚本 - 基于种间共线性分析结果
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echo "=========================================="
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echo "开始 KaKs 分析"
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echo "=========================================="
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# 步骤 1: 创建目录
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mkdir -p /home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822/kaks_analysis
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# 步骤 2: 提取同源对
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echo "[1/4] 从种间共线性分析中提取 SPL 同源对..."
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python3 << 'PYEOF'
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import re
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# 读取 SPL 基因 ID
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with open('/home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822/final/Ft.SPL.final_members.id') as f:
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spl_ids = [line.strip() for line in f]
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# 从 collinearity 文件中提取同源对
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pairs = []
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with open('/home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822/interspecies_synteny/analysis/Ft_Ath.collinearity') as f:
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for line in f:
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match = re.match(r'\s*\d+-\s*\d+:\s+(\S+)\s+(\S+)', line)
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if match:
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ath_id = match.group(1)
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ft_id = match.group(2)
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if ft_id in spl_ids:
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pairs.append((ft_id, ath_id))
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# 去重并写入文件
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pairs = sorted(set(pairs))
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with open('/home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822/kaks_analysis/ortholog_pairs.txt', 'w') as f:
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for ft_id, ath_id in pairs:
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f.write(f"{ft_id}\t{ath_id}\n")
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print(f"找到 {len(pairs)} 对同源基因")
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PYEOF
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# 步骤 3: 提取序列
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echo "[2/4] 提取 SPL 家族序列..."
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python3 << 'PYEOF'
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import re
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WORKSPACE = "/home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822"
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INPUT = "/home/xia-lab/wutx/00test/bbav20311/input/job_1774180111822"
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KAKS_DIR = f"{WORKSPACE}/kaks_analysis"
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# 读取 SPL 基因 ID
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with open(f'{WORKSPACE}/final/Ft.SPL.final_members.id') as f:
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spl_ids = set(line.strip() for line in f)
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# 提取函数
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def extract_fasta(input_file, output_file, target_ids):
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count = 0
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with open(input_file) as infile, open(output_file, 'w') as outfile:
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write_flag = False
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for line in infile:
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if line.startswith('>'):
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gene_id = line[1:].split()[0]
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write_flag = False
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for spl_id in target_ids:
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if gene_id.startswith(spl_id.split('.')[0]):
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write_flag = True
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count += 1
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outfile.write(line)
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break
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elif write_flag:
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outfile.write(line)
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return count
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# 提取 Ft 序列
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extract_fasta(f'{INPUT}/Ft.cds.fasta', f'{KAKS_DIR}/Ft.SPL.cds.fasta', spl_ids)
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extract_fasta(f'{INPUT}/Ft.pep.fasta', f'{KAKS_DIR}/Ft.SPL.pep.fasta', spl_ids)
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# 获取 Ath 基因
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ath_genes = set()
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with open(f'{KAKS_DIR}/ortholog_pairs.txt') as f:
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for line in f:
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parts = line.strip().split('\t')
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if len(parts) == 2:
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ath_genes.add(parts[1])
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# 提取 Ath 序列
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extract_fasta(f'{INPUT}/Ath.cds.fasta', f'{KAKS_DIR}/Ath.SPL.cds.fasta', ath_genes)
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extract_fasta(f'{INPUT}/Ath.pep.fasta', f'{KAKS_DIR}/Ath.SPL.pep.fasta', ath_genes)
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print("序列提取完成")
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PYEOF
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# 步骤 4: 运行 KaKs
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echo "[3/4] 运行 KaKs 分析..."
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cd /home/xia-lab/wutx/00test/bbav20311
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/home/xia-lab/miniconda3/bin/conda run -n test4py311 \
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python apps/cli/run_kaks_v2.py \
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-o workspace/job_1774180111822/kaks \
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-p Ft.SPL \
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--cds1 workspace/job_1774180111822/kaks_analysis/Ft.SPL.cds.fasta \
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--cds2 workspace/job_1774180111822/kaks_analysis/Ath.SPL.cds.fasta \
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--pep1 workspace/job_1774180111822/kaks_analysis/Ft.SPL.pep.fasta \
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--pep2 workspace/job_1774180111822/kaks_analysis/Ath.SPL.pep.fasta \
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--pairs workspace/job_1774180111822/kaks_analysis/ortholog_pairs.txt \
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--neutral-rate 7.08e-9
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# 步骤 5: 验证结果已自动复制到 final 目录
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echo "[4/4] 验证结果..."
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echo "结果已自动复制到 final 目录（由 run_kaks_v2.py 完成）"
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echo ""
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echo "=========================================="
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echo "KaKs 分析完成！"
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echo "=========================================="
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echo ""
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echo "结果文件："
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ls -lh /home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822/final/ | grep kaks
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echo ""
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echo "绘图文件："
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ls -lh /home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822/final/ | grep -E "\.pdf|\.png"
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echo ""
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echo "结果预览："
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cat /home/xia-lab/wutx/00test/bbav20311/workspace/job_1774180111822/final/Ft.SPL.kaks_results.csv
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