I have file names like:
5_END_1033_ACAGTG_L002_R1_001.fastq.gz 5_END_1033_ACAGTG_L002_R2_001.fastq.gz 40_END_251_GTGAAA_L002_R1_001.fastq.gz 40_END_251_GTGAAA_L002_R2_001.fastq.gz
I want something like:
END_1033_R1.fastq.gz END_1033_R2.fastq.gz END_251_R1.fastq.gz END_251_R2.fastq.gz
Are there good ways to rename these files in linux?
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Answer
You could try using a loop to extract the important part of the filename:
for file in ./*.gz; do newname=$(echo $file | sed -re 's/^([^ACAGTG]+).*(R[1-3]).*/12.fastq.gz/g'); echo $newname; done
This will simply give you a new list of filenames. You can then move them:
for file in ./*.gz; do newname=$(echo $file | sed -re 's/^([^ACAGTG]+).*(R[1-3]).*/12.fastq.gz/g'); mv $file $newname; done
To break this down a little:
- loop over the *.gz files
- create a variable which strips out the unnecessary content from the name
- move the file name to that new name
I expect there are better ways to do this, but it’s what I came up with off the top of my head.
Test:
$ ls 40_END_251_GTGAAA_L002_R1_001.fastq.gz 40_END_251_GTGAAA_L002_R2_001.fastq.gz 5_END_1033_ACAGTG_L002_R1_001.fastq.gz 5_END_1033_ACAGTG_L002_R2_001.fastq.gz $ for file in ./*.gz; do newname=$(echo $file | sed -re 's/^([^ACAGTG]+).*(R[1-3]).*/12.fastq.gz/g'); echo $newname; done ./40_END_251_R1.fastq.gz ./40_END_251_R2.fastq.gz ./5_END_1033_R1.fastq.gz ./5_END_1033_R2.fastq.gz $ for file in ./*.gz; do newname=$(echo $file | sed -re 's/^([^ACAGTG]+).*(R[1-3]).*/12.fastq.gz/g'); mv $file $newname; done $ ls 40_END_251_R1.fastq.gz 40_END_251_R2.fastq.gz 5_END_1033_R1.fastq.gz 5_END_1033_R2.fastq.gz
Note I’m doing this in bash 4.4.5
EDIT
Given I’m not entirely sure which columns in the name are the most important, awk might work better:
for file in ./*.gz; do newname=$(echo $file | awk -F'_' '{print $2 "_" $3 "_" $6}' -); echo $newname; done
This will split the filename by _ and allow you to reference the columns you want using $X:
for file in ./*.gz; do newname=$(echo $file | awk -F'_' '{print $2 "_" $3 "_" $6}' -); mv $file "${newname}.fastq.gz"; done