Renaming long file names in bulk - linux

Question

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?

Answer 1

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]).*/\1\2\.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]).*/\1\2\.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]).*/\1\2\.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]).*/\1\2\.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