shell脚本批量对文件改名(名字新旧不相关)

首先，要用到数组，请先看关于数组的基础知识

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要求：把电脑中的SRR开头的文件名改为容易识别的Library_Name

电脑中的SRR文件如下：

SRR文件

Run和Library_Name的对应关系如下
也就是要以第二列代替第三列，所以简单的rename命令不行，因为这些名字之间㐊简单的替换

SAMN09837892    Lib_FUSCCTNBC158.TT_WES SRR7696207      FUSCCTNBC158_FrozenPrimaryTumorTissue
SAMN09838014    Lib_FUSCCTNBC337.TT_WES SRR8517853      FUSCCTNBC337_FrozenPrimaryTumorTissue
SAMN09837870    Lib_FUSCCTNBC123.TT_WES SRR8517854      FUSCCTNBC123_FrozenPrimaryTumorTissue
SAMN09837938    Lib_FUSCCTNBC228.TT_WES SRR8517855      FUSCCTNBC228_FrozenPrimaryTumorTissue
SAMN09837940    Lib_FUSCCTNBC230.TT_WES SRR8517856      FUSCCTNBC230_FrozenPrimaryTumorTissue
SAMN09837941    Lib_FUSCCTNBC233.TT_WES SRR8517857      FUSCCTNBC233_FrozenPrimaryTumorTissue
SAMN09837942    Lib_FUSCCTNBC234.TT_WES SRR8517858      FUSCCTNBC234_FrozenPrimaryTumorTissue
SAMN09837934    Lib_FUSCCTNBC220.TT_WES SRR8517859      FUSCCTNBC220_FrozenPrimaryTumorTissue
SAMN09837935    Lib_FUSCCTNBC223.TT_WES SRR8517860      FUSCCTNBC223_FrozenPrimaryTumorTissue
SAMN09837936    Lib_FUSCCTNBC225.TT_WES SRR8517861      FUSCCTNBC225_FrozenPrimaryTumorTissue
SAMN09837937    Lib_FUSCCTNBC227.TT_WES SRR8517862      FUSCCTNBC227_FrozenPrimaryTumorTissue
SAMN09837943    Lib_FUSCCTNBC235.TT_WES SRR8517863      FUSCCTNBC235_FrozenPrimaryTumorTissue
SAMN09837944    Lib_FUSCCTNBC236.TT_WES SRR8517864      FUSCCTNBC236_FrozenPrimaryTumorTissue
SAMN09838036    Lib_FUSCCTNBC387.TT_WES SRR8517865      FUSCCTNBC387_FrozenPrimaryTumorTissue
SAMN09838037    Lib_FUSCCTNBC389.TT_WES SRR8517866      FUSCCTNBC389_FrozenPrimaryTumorTissue
SAMN09838032    Lib_FUSCCTNBC380.TT_WES SRR8517867      FUSCCTNBC380_FrozenPrimaryTumorTissue
SAMN09838033    Lib_FUSCCTNBC383.TT_WES SRR8517868      FUSCCTNBC383_FrozenPrimaryTumorTissue
SAMN09838077    Lib_FUSCCTNBC440.TT_WES SRR8517869      FUSCCTNBC440_FrozenPrimaryTumorTissue
SAMN09838075    Lib_FUSCCTNBC438.TT_WES SRR8517870      FUSCCTNBC438_FrozenPrimaryTumorTissue
SAMN09837967    Lib_FUSCCTNBC262.TT_WES SRR8517871      FUSCCTNBC262_FrozenPrimaryTumorTissue
SAMN09837968    Lib_FUSCCTNBC263.TT_WES SRR8517872      FUSCCTNBC263_FrozenPrimaryTumorTissue
SAMN09837965    Lib_FUSCCTNBC260.TT_WES SRR8517873      FUSCCTNBC260_FrozenPrimaryTumorTissue

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提示

• 1根据上面的对应关系，首先创建( touch)这些gz文件出来
• 2 然后 shell脚本改名
  比如SRR7696207改为Lib_FUSCCTNBC158.TT_WES

1 创建gz文件

先写入上述第二个表的文件

cat >tmp
SAMN09837892    Lib_FUSCCTNBC158.TT_WES SRR7696207      FUSCCTNBC158_FrozenPrimaryTumorTissue
SAMN09838014    Lib_FUSCCTNBC337.TT_WES SRR8517853      FUSCCTNBC337_FrozenPrimaryTumorTissue
SAMN09837870    Lib_FUSCCTNBC123.TT_WES SRR8517854      FUSCCTNBC123_FrozenPrimaryTumorTissue
SAMN09837938    Lib_FUSCCTNBC228.TT_WES SRR8517855      FUSCCTNBC228_FrozenPrimaryTumorTissue
SAMN09837940    Lib_FUSCCTNBC230.TT_WES SRR8517856      FUSCCTNBC230_FrozenPrimaryTumorTissue
.....

创建1.fastq.gz和2.fastq.gz文件

cat tmp|cut -f3|while read id;do touch ${id}_{1,2}.fastq.gz;done

或者

cat config|awk '{print$3}'|while read id;do touch ${id}_{1,2}.fastq.gz;done

ls
SRR6269851_1.fastq.gz  SRR6269859_1.fastq.gz  SRR6269867_1.fastq.gz  SRR6269875_1.fastq.gz  SRR8517854_1.fastq.gz  SRR8517862_1.fastq.gz  SRR8517870_1.fastq.gz
SRR6269851_2.fastq.gz  SRR6269859_2.fastq.gz  SRR6269867_2.fastq.gz  SRR6269875_2.fastq.gz  SRR8517854_2.fastq.gz  SRR8517862_2.fastq.gz  SRR8517870_2.fastq.gz
SRR6269852_1.fastq.gz  SRR6269860_1.fastq.gz  SRR6269868_1.fastq.gz  SRR6269876_1.fastq.gz  SRR8517855_1.fastq.gz  SRR8517863_1.fastq.gz  SRR8517871_1.fastq.gz
SRR6269852_2.fastq.gz  SRR6269860_2.fastq.gz  SRR6269868_2.fastq.gz  SRR6269876_2.fastq.gz

2重命名

cat tmp|while read id 
do 
arr=($id) 
Lib_name=${arr[1]}
SRR_name=${arr[2]}
echo $Lib_name echo $SRR_name
mv ${SRR_name}_1.fastq.gz ${Lib_name}_1.fastq.gz
mv ${SRR_name}_2.fastq.gz ${Lib_name}_2.fastq.gz
done

解释如下

• 1 arr=($id)
  把read到的id也就是tmp的所有数据放在了名为arr数组里，()的作用就是建立数组
• 2 arr[1]读取arr第2列，命名为Lib_name
  arr[12]读取arr第3列，命名为SRR_name

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