Linux學習6之shell篩選當前目錄下檔案並逐個對其進行操作
阿新 • • 發佈：2019-02-19
程式碼：
注意，當前目錄下最好不要有其他不相關的檔名包含“sam”的檔案！！！hadoop@Master:~/cloud/adam/xubo/code$ cat a.sh #!/bin/bash #SRR003161h20t1 #samtools view -h -S SRR003161h20t1.sam >SRR003161h20t1.bam #samtools sort -o SRR003161h20t1.sorted.bam SRR003161h20t1.bam #samtools view -h -S SRR003161h20t1.sam |samtools sort -o SRR003161h20t1Sort.bam # samtools sort -o toy.sorted.bam toy.bam dir=$(ls -l ./ |awk '!/^d/ {print $NF}' |grep -i "sam" ) for i in $dir do #echo $i startTime=`date +"%s.%N"` s1=$(echo $i | cut -d '.' -f 1) samtools view -h -S $i |samtools sort -o $s1.sort.bam endTime=`date +"%s.%N"` echo $i" "`awk -v x1="$(echo $endTime | cut -d '.' -f 1)" -v x2="$(echo $startTime | cut -d '.' -f 1)" -v y1="$[$(echo $endTime | cut -d '.' -f 2) / 1000]" -v y2="$[$(echo $startTime | cut -d '.' -f 2) /1000]" 'BEGIN{printf " RunTIme:%.6f s",(x1-x2)+(y1-y2)/1000000}'` done
執行語句：
hadoop@Mcnode4:~/cloud/adam/xubo/data/test20160310/bwa3sh/test<span style="font-size: 13.3333px; font-family: Arial, Helvetica, sans-serif;">142234</span><span style="font-size: 12px; font-family: Arial, Helvetica, sans-serif;">$ ./a.sh &> s2bambwaMcnode4T201603152115.txt</span>
執行結果：
hadoop@Mcnode4:~/cloud/adam/xubo/data/test20160310/bwa3sh/test142234$ cat s2bambwaMcnode4201603152104.txt SRR003161h100000t1.sam RunTIme:2.245094 s SRR003161h100000t2.sam RunTIme:2.248639 s SRR003161h100000t3.sam RunTIme:2.258191 s SRR003161h10000t1.sam RunTIme:0.286576 s SRR003161h10000t2.sam RunTIme:0.275169 s SRR003161h10000t3.sam RunTIme:0.280443 s ./a.sh: line 17: 087064391: value too great for base (error token is "087064391") SRR003161h1000t2.sam ./a.sh: line 17: 093253589: value too great for base (error token is "093253589") SRR003161h1000t3.sam SRR003161h20t1.sam RunTIme:0.050949 s SRR003161h20t2.sam RunTIme:0.058536 s SRR003161h20t3.sam RunTIme:0.041384 s [bam_sort_core] merging from 3 files... SRR003161t1.sam RunTIme:164.763129 s [bam_sort_core] merging from 3 files... SRR003161t2.sam RunTIme:166.538254 s [bam_sort_core] merging from 3 files... hadoop@Mcnode4:~/cloud/adam/xubo/data/test20160310/bwa3sh/test142234$ ll -h total 6.7G drwxrwxr-x 3 hadoop hadoop 4.0K 3月 15 21:10 ./ drwxrwxr-x 4 hadoop hadoop 4.0K 3月 15 19:39 ../ -rwx------ 1 hadoop hadoop 797 3月 15 21:02 a.sh* drwxrwxr-x 2 hadoop hadoop 4.0K 3月 15 20:17 fff/ -rw-rw-r-- 1 hadoop hadoop 776 3月 15 21:10 s2bambwaMcnode4201603152104.txt -rwx------ 1 hadoop hadoop 4.8K 3月 15 20:09 s2b.sh* -rwx------ 1 hadoop hadoop 354 3月 15 20:18 showDirectory.sh* -rwx------ 1 hadoop hadoop 450 3月 15 20:25 showFileAndDirectory.sh* -rw-rw-r-- 1 hadoop hadoop 106K 3月 14 22:40 SRR003161h100000t1.sai -rw-rw-r-- 1 hadoop hadoop 29M 3月 14 22:41 SRR003161h100000t1.sam -rw-rw-r-- 1 hadoop hadoop 9.5M 3月 15 21:04 SRR003161h100000t1.sort.bam -rw-rw-r-- 1 hadoop hadoop 106K 3月 14 22:48 SRR003161h100000t2.sai -rw-rw-r-- 1 hadoop hadoop 29M 3月 14 22:49 SRR003161h100000t2.sam -rw-rw-r-- 1 hadoop hadoop 9.5M 3月 15 21:04 SRR003161h100000t2.sort.bam -rw-rw-r-- 1 hadoop hadoop 106K 3月 14 22:57 SRR003161h100000t3.sai -rw-rw-r-- 1 hadoop hadoop 29M 3月 14 22:58 SRR003161h100000t3.sam -rw-rw-r-- 1 hadoop hadoop 9.5M 3月 15 21:04 SRR003161h100000t3.sort.bam -rw-rw-r-- 1 hadoop hadoop 11K 3月 14 22:38 SRR003161h10000t1.sai -rw-rw-r-- 1 hadoop hadoop 3.0M 3月 14 22:39 SRR003161h10000t1.sam -rw-rw-r-- 1 hadoop hadoop 1001K 3月 15 21:04 SRR003161h10000t1.sort.bam -rw-rw-r-- 1 hadoop hadoop 11K 3月 14 22:46 SRR003161h10000t2.sai -rw-rw-r-- 1 hadoop hadoop 3.0M 3月 14 22:47 SRR003161h10000t2.sam -rw-rw-r-- 1 hadoop hadoop 1001K 3月 15 21:04 SRR003161h10000t2.sort.bam -rw-rw-r-- 1 hadoop hadoop 11K 3月 14 22:54 SRR003161h10000t3.sai -rw-rw-r-- 1 hadoop hadoop 3.0M 3月 14 22:55 SRR003161h10000t3.sam -rw-rw-r-- 1 hadoop hadoop 1001K 3月 15 21:04 SRR003161h10000t3.sort.bam -rw-rw-r-- 1 hadoop hadoop 1.1K 3月 14 22:36 SRR003161h1000t1.sai -rw-rw-r-- 1 hadoop hadoop 1.1K 3月 14 22:44 SRR003161h1000t2.sai -rw-rw-r-- 1 hadoop hadoop 339K 3月 14 22:45 SRR003161h1000t2.sam -rw-rw-r-- 1 hadoop hadoop 111K 3月 15 21:04 SRR003161h1000t2.sort.bam -rw-rw-r-- 1 hadoop hadoop 1.1K 3月 14 22:52 SRR003161h1000t3.sai -rw-rw-r-- 1 hadoop hadoop 339K 3月 14 22:53 SRR003161h1000t3.sam -rw-rw-r-- 1 hadoop hadoop 111K 3月 15 21:04 SRR003161h1000t3.sort.bam -rw-rw-r-- 1 hadoop hadoop 22K 3月 15 20:07 SRR003161h20t1.bam -rw-rw-r-- 1 hadoop hadoop 88 3月 14 22:34 SRR003161h20t1.sai -rw-rw-r-- 1 hadoop hadoop 22K 3月 14 22:35 SRR003161h20t1.sam -rw-rw-r-- 1 hadoop hadoop 9.0K 3月 15 21:04 SRR003161h20t1.sort.bam -rw-rw-r-- 1 hadoop hadoop 9.0K 3月 15 20:07 SRR003161h20t1Sort.bam -rw-rw-r-- 1 hadoop hadoop 88 3月 14 22:42 SRR003161h20t2.sai -rw-rw-r-- 1 hadoop hadoop 22K 3月 14 22:43 SRR003161h20t2.sam -rw-rw-r-- 1 hadoop hadoop 9.0K 3月 15 21:04 SRR003161h20t2.sort.bam -rw-rw-r-- 1 hadoop hadoop 88 3月 14 22:50 SRR003161h20t3.sai -rw-rw-r-- 1 hadoop hadoop 22K 3月 14 22:51 SRR003161h20t3.sam -rw-rw-r-- 1 hadoop hadoop 9.0K 3月 15 21:04 SRR003161h20t3.sort.bam -rw-rw-r-- 1 hadoop hadoop 36M 3月 15 19:58 SRR003161t1.bam -rw-rw-r-- 1 hadoop hadoop 5.7M 3月 14 23:53 SRR003161t1.sai -rw-rw-r-- 1 hadoop hadoop 1.6G 3月 15 00:09 SRR003161t1.sam -rw-rw-r-- 1 hadoop hadoop 513M 3月 15 21:06 SRR003161t1.sort.bam -rw-rw-r-- 1 hadoop hadoop 5.7M 3月 15 01:04 SRR003161t2.sai -rw-rw-r-- 1 hadoop hadoop 1.6G 3月 15 01:21 SRR003161t2.sam -rw-rw-r-- 1 hadoop hadoop 513M 3月 15 21:09 SRR003161t2.sort.bam -rw-rw-r-- 1 hadoop hadoop 5.7M 3月 15 02:17 SRR003161t3.sai -rw-rw-r-- 1 hadoop hadoop 1.6G 3月 15 02:32 SRR003161t3.sam -rw-rw-r-- 1 hadoop hadoop 389M 3月 15 21:12 SRR003161t3.sort.bam -rw-rw-r-- 1 hadoop hadoop 272M 3月 15 21:10 STDIN.tmp.0000.bam -rw-rw-r-- 1 hadoop hadoop 256M 3月 15 21:10 STDIN.tmp.0001.bam -rw-rw-r-- 1 hadoop hadoop 31M 3月 15 21:10 STDIN.tmp.0002.bam -rwx------ 1 hadoop hadoop 276 3月 15 20:07 te.sh* -rw------- 1 hadoop hadoop 12K 3月 15 20:03 .te.sh.swp