Linux学习6之shell筛选当前目录下文件并逐个对其进行操作

linux-dash

A beautiful web dashboard for Linux

项目地址：https://gitcode.com/gh_mirrors/li/linux-dash

免费下载资源

KeepLearningBigData

5732人浏览 · 2016-03-15 21:13:56

KeepLearningBigData · 2016-03-15 21:13:56 发布

代码：

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

注意，当前目录下最好不要有其他不相关的文件名包含“sam”的文件！！！

运行语句：

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>

运行结果：

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

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A beautiful web dashboard for Linux

最近提交(Master分支：3 个月前 )

186a802e added ecosystem file for PM2 4 年前

5def40a3 Add host customization support for the NodeJS version 4 年前

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