图1
1.找出与参考相同区域
python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig1/vcf_stat_vs_refgenome.py -i all.chr.vcf -o 125K_vcf_stat_vs_refgenome --min-length 125K --max-gap 5M --filtered-min-length 125K
2.绘图
for i in `ls *mian*txt`;do echo ${i%.txt};python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig1/125K_vcf_stat_vs_refgenome/1v30324-api.py -i1 $i -i2 chr_len.txt -o fig1.${i%.txt}.png ;done
图2
1.找出和指定样品相同区域
for i in mianhua13 mianhua4 Simian3hao;do python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig2/vcf_stat_vs_onesample.py -i ../all.chr.vcf -o 125k_vcf_stat_vs_${i} --ref-sample $i --min-length 125K --max-gap 5M & done # 125K
for i in mianhua4 mianhua13 Simian3hao;do python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig2/vcf_stat_vs_onesample.py -i ../all.chr.vcf -o 500k_vcf_stat_vs_${i} --ref-sample $i --min-length 125K --max-gap 5M --filtered-min-length 500K & done # 500K
2.合并为一个表格
python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig2/500k_vcf_stat_vs_Simian3hao/test/web-r1-merge_intervals.py -i mianhua245144-1_vs_*.txt -o merged_output.txt
3.绘图
python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig2/500k_vcf_stat_vs_Simian3hao/test/fi2plot.py -i1 merged_output.txt -i2 chr_len.txt -o output.png
for j in darwinii Simian3hao mianhua4 mianhua13 ;do echo $j ; for i in mianhua245144-1 mianhua245145-3 mianhua245146-1 mianhua245146-3 mianhua245148-1 mianhua245148-2 sujimian211;do ll ../500k_vcf_stat_vs_${j}/$i.txt ;cp ../500k_vcf_stat_vs_${j}/$i.txt ${i}_vs_${j}.txt; done;done
for i in mianhua245144-1 mianhua245145-3 mianhua245146-1 mianhua245146-3 mianhua245148-1 mianhua245148-2 sujimian211;do python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig2/500k_vcf_stat_vs_Simian3hao/test/001web-r1-merge_intervals.py -i ${i}_vs_*.txt -o ${i}_merged_output.txt;done
for i in mianhua245144-1 mianhua245145-3 mianhua245146-1 mianhua245146-3 mianhua245148-1 mianhua245148-2 sujimian211;do python3 /share/nas2/yuj/project/2025/re-sequencing/GP-20241021-9521-2_20250104/02daerwenshimian/20250325plot/fig2/500k_vcf_stat_vs_Simian3hao/test/fi2plot.py -i1 ${i}_merged_output.txt -i2 chr_len.txt -o fig2.${i}.png ;done