linux shell 統計plink格式樣本缺失率
阿新 • • 發佈：2021-10-31
1、shell指令碼
[root@centos79 test]# cat test.sh #!/bin/bash ## step1 for i in $(seq `sed -n "$=" $1`); do sed -n "$i"p $1 | cut -d " " -f 7- | grep -o "0" | wc -l >> result1; done echo "step1 done!" ## step2 paste result1 $1 | awk '{OFS = "\t"} {print $3, $1/2, $1/(NF - 7)}' > result.txt rm -f result1 echo"step2 done!" ## step3 sed '1i id\tmisssite\trate' result.txt -i echo "finished!"
2、測試資料、及測試
[root@centos79 test]# ls outcome.map outcome.ped test.sh [root@centos79 test]# cat outcome.map 1 snp1 0 55910 1 snp2 0 85204 1 snp3 0 122948 1 snp4 0 2037501 snp5 0 312707 1 snp6 0 356863 1 snp7 0 400518 1 snp8 0 487423 [root@centos79 test]# cat outcome.ped DOR 1 0 0 0 -9 G G 0 0 0 0 0 0 A A T T G G 0 0 DOR 2 0 0 0 -9 0 0 G G 0 0 0 0 A A T T A G 0 0 DOR 3 0 0 0 -9 0 0 C C 0 0 G G G G T T A G 0 0 DOR 4 0 0 0 -9 0 0 C C 0 0 G G G G A A G G G G DOR5 0 0 0 -9 G G C C 0 0 G G G G A A A G G C DOR 6 0 0 0 -9 G G C C 0 0 G G G G A A A A C C [root@centos79 test]# bash test.sh outcome.ped step1 done! step2 done! finished! [root@centos79 test]# ls outcome.map outcome.ped result.txt test.sh [root@centos79 test]# cat result.txt id misssite rate 1 4 0.5 2 4 0.5 3 3 0.375 4 2 0.25 5 1 0.125 6 1 0.125
3、plink驗證
[root@centos79 test]# ls outcome.map outcome.ped result.txt test.sh [root@centos79 test]# plink --file outcome --missing --out verify > /dev/null; rm *.log *.nosex [root@centos79 test]# ls outcome.map outcome.ped result.txt test.sh verify.imiss verify.lmiss [root@centos79 test]# cat verify.imiss FID IID MISS_PHENO N_MISS N_GENO F_MISS DOR 1 Y 4 8 0.5 DOR 2 Y 4 8 0.5 DOR 3 Y 3 8 0.375 DOR 4 Y 2 8 0.25 DOR 5 Y 1 8 0.125 DOR 6 Y 1 8 0.125 [root@centos79 test]# cat result.txt id misssite rate 1 4 0.5 2 4 0.5 3 3 0.375 4 2 0.25 5 1 0.125 6 1 0.125