绘制染色体上同源区段

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