linux脚本重命名文件,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

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

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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