How to remove [ACTG] from file names in bash

Question

[v.berriosfarias]

Hello i have several files which names have the following pattern

VIR3A_CCGCGGTT-CTAGCGCT_L00M_R1_001.fastq.gz 

VIR3Q_TAATACAG-GTGAATAT_L00M_R2_001.fastq.gz

 VIR4J_CGTTAGAA-GACCTGAA_L00M_R1_001.fastq.gz

I want to cut all the substrings which have ACTG. This is the desired output:

VIR3A_L00M_R1_001.fastq.gz 

VIR3Q_L00M_R2_001.fastq.gz

 VIR4J_L00M_R1_001.fastq.gz

how can I do that?

Thanks for your time :)

[Pierre Lindenbaum]

why is it an issue ?

[v.berriosfarias]

I'm trying to change the file names to the mentioned desired ones, there are like 40 of the files with the same pattern of ACTG elements

Answer 1

[JC]

$ for F in *fastq.gz; do mv $F $(echo $F | perl -pe 's/_[ACGT]+?-[ACGT]+?_/_/'); done
mv VIR3A_CCGCGGTT-CTAGCGCT_L00M_R1_001.fastq.gz VIR3A_L00M_R1_001.fastq.gz
mv VIR3Q_TAATACAG-GTGAATAT_L00M_R2_001.fastq.gz VIR3Q_L00M_R2_001.fastq.gz
mv VIR4J_CGTTAGAA-GACCTGAA_L00M_R1_001.fastq.gz VIR4J_L00M_R1_001.fastq.gz

Answer 2

[cpad0112]

with rename:

$ rename -n 's/_[ATGC]*-[ATGC]*//' *.gz

'VIR3A_CCGCGGTT-CTAGCGCT_L00M_R1_001.fastq.gz' would be renamed to 'VIR3A_L00M_R1_001.fastq.gz'
'VIR3Q_TAATACAG-GTGAATAT_L00M_R2_001.fastq.gz' would be renamed to 'VIR3Q_L00M_R2_001.fastq.gz'
'VIR4J_CGTTAGAA-GACCTGAA_L00M_R1_001.fastq.gz' would be renamed to 'VIR4J_L00M_R1_001.fastq.gz'

Remove -n once you are satisfied with dry-run.

with parallel:

$ parallel --plus --dry-run cp {} {=s/_\[ATGC\]+-\[ATGC\]+//=} ::: *.gz

cp VIR3A_CCGCGGTT-CTAGCGCT_L00M_R1_001.fastq.gz VIR3A_L00M_R1_001.fastq.gz
cp VIR3Q_TAATACAG-GTGAATAT_L00M_R2_001.fastq.gz VIR3Q_L00M_R2_001.fastq.gz
cp VIR4J_CGTTAGAA-GACCTGAA_L00M_R1_001.fastq.gz VIR4J_L00M_R1_001.fastq.gz

Remove dry-run if you are okay with output from dry run.

in bash shell (and sed):

$ for i in *.gz; do output=$(echo $i| sed 's/_[ATGC]*-[ATGC]*//'); echo cp $i $output; done

cp VIR3A_CCGCGGTT-CTAGCGCT_L00M_R1_001.fastq.gz VIR3A_L00M_R1_001.fastq.gz
cp VIR3Q_TAATACAG-GTGAATAT_L00M_R2_001.fastq.gz VIR3Q_L00M_R2_001.fastq.gz
cp VIR4J_CGTTAGAA-GACCTGAA_L00M_R1_001.fastq.gz VIR4J_L00M_R1_001.fastq.gz

Remove second echo if you are okay with dry-run.

[JC]

FYI, rename command is not a basic Linux tool, it needs to be installed with apt, yum, pacman, ...