linux 基本命令___0003 字符串处理和yum安装软件的路径

字符串变量的处理

参考链接：SHELL字符串处理技巧

计算字符串的字符数量: ${#str}

str="xxx-Lane1_S2_L001_R1_trim.fastq"

echo $str
### xxx-Lane1_S2_L001_R1_trim.fastq

echo ${#str}
### 31

删除VALUE字符串中以分隔符“.”匹配的右边字符，保留左边字符: ${str%.*}或${str%%.*}

str2=`ls xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz`

echo ${str2%.*} #单次匹配
### xxx-Lane1_S2_L001_R1_trim.fastq.tar

echo ${str2%%.*} #多次匹配
### xxx-Lane1_S2_L001_R1_trim

删除VALUE字符串中以分隔符“.”匹配的左边字符，保留右边字符: ${str#*.}或${str##*.}

str2=`ls xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz`

echo ${str2#*.}
### fastq.tar.gz

echo ${str2##*.}
### .gz

用NEW子串替换str字符串中匹配的OLD子串: ${str/OLD/NEW}或${str//OLD/NEW}

str2=`ls xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz`

echo ${str2/tar.gz/bz}
### xxx-Lane1_S2_L001_R1_trim.fastq.bz

echo ${str3//_/|}
### xxx-Lane1|S2|L001|R1|trim.fastq.tar.gz

“*”表示通配符，用于匹配字符串将被删除的字串
非贪婪匹配：

• “%”表示从右向左匹配；
• “#”表示从左向右匹配；
• “/”表示替换

贪婪匹配：

• “%%”表示从右向左匹配；
• “##”表示从左向右匹配；
• “//”表示替换

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从str字符串的左边开始中截取子串: ${str:OFFSET}或${str:OFFSET:LENGTH}

str2=`ls xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz`

echo ${str2:4:8}
### Lane1_S2

echo ${str2:4}
### Lane1_S2_L001_R1_trim.fastq.tar.gz

从str字符串的右边开始中截取子串: ${str:0-OFFSET}或${str:0-OFFSET:LENGTH}

str2=`ls xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz`

echo ${str2:4:8}
### Lane1_S2

echo ${str2:0-6}
### tar.gz

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下例中，WORD可以为一个字符串，也可以为一个变量。当为变量时，需要用“$”引用该变量。

var="xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz"
word="yyy"
str=""

# 1.  ${VALUE:-WORD}：当变量未定义或者值为空时，返回值为WORD的内容，否则返回变量的值。
echo ${str:-$word}
### yyy

echo ${var:-$word}
### xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz

# 2.  ${VALUE:=WORD}：当变量未定义或者值为空时，返回WORD的值的同时并将WORD赋值给VALUE，否则返回变量的值。
echo ${str:=$word}
### yyy
echo $str #此时str的值也发生了改变
### yyy

echo ${var:=$word}
### xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz

# 3.  ${VALUE:+WORD}：当变量已赋值时，其值才用WORD替换，否则不进行任何替换。
echo ${str:+$word}
###     

echo ${var:+$word}
yyy

# 4.  ${VALUE:?MESSAGE}：当变量已赋值时，正常替换。否则将消息MESSAGE送到标准错误输出（若此替换出现在SHELL程序中，那么该程序将终止运行）。
echo ${str:?"warning"}
### bash: str: warning

echo ${var:?"warning"}
### xxx-Lane1_S2_L001_R1_trim.fastq.tar.gz

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yum安装软件的路径

以安装BEDTools为例

#
sudo yum install BEDTools

rpm -q BEDTools
#BEDTools-2.15.0-1.el6.x86_64

rpm -qa |grep BEDTools
#BEDTools-2.15.0-1.el6.x86_64

rpm -ql BEDTools-2.15.0-1.el6.x86_64
# /usr/bin/annotateBed
# /usr/bin/bamToBed
# /usr/bin/bed12ToBed6
# /usr/bin/bedToBam
# /usr/bin/bedToIgv
# /usr/bin/bedpeToBam
# /usr/bin/bedtools
# /usr/bin/closestBed
# /usr/bin/clusterBed
# /usr/bin/complementBed
# /usr/bin/coverageBed
# /usr/bin/fastaFromBed
# /usr/bin/flankBed
# /usr/bin/genomeCoverageBed
# /usr/bin/getOverlap
# /usr/bin/groupBy
# /usr/bin/intersectBed
# /usr/bin/linksBed
# /usr/bin/maskFastaFromBed
# /usr/bin/mergeBed
# /usr/bin/multiBamCov
# /usr/bin/multiIntersectBed
# /usr/bin/nucBed
# /usr/bin/pairToBed
# /usr/bin/pairToPair
# /usr/bin/shuffleBed
# /usr/bin/slopBed
# /usr/bin/sortBed
# /usr/bin/subtractBed
# /usr/bin/tagBam
# /usr/bin/unionBedGraphs
# /usr/bin/windowBed
# /usr/bin/windowMaker
# /usr/share/BEDTools
# /usr/share/BEDTools/data
# /usr/share/BEDTools/data/knownGene.hg18.chr21.bed
# /usr/share/BEDTools/data/rmsk.hg18.chr21.bed
# /usr/share/BEDTools/genomes
# /usr/share/BEDTools/genomes/human.hg18.genome
# /usr/share/BEDTools/genomes/human.hg19.genome
# /usr/share/BEDTools/genomes/mouse.mm8.genome
# /usr/share/BEDTools/genomes/mouse.mm9.genome
# /usr/share/doc/BEDTools-2.15.0
# /usr/share/doc/BEDTools-2.15.0/LICENSE
# /usr/share/doc/BEDTools-2.15.0/README.rst
# /usr/share/doc/BEDTools-2.15.0/RELEASE_HISTORY

RPM

rpm 全名是 “RedHat Package Manager”，简称则为RPM。
RPM默认安装路径：

• /etc 设置文件放置的目录
• /usr/bin 可执行文件
• /usr/lib 程序使用的动态函数库
• /usr/share/doc 基本的软件使用手册与帮助文档
• /usr/share/man man page文件