Remove a part of a filename in a Bash loop

[Marius]

I have many files named like this:

lib01.GFBAG_UHAU.fastq.sam.bam
lib02.ABABAB_ZU.fastq.sam.bam
lib03.ZGAZG_IAUDH.fastq.sam.bam

Many parts of the filenames are thus variable in length, although they are connected through the same type of punctuation (. or _).
What I want to achieve is to remove the part .fastq.sam.bam from a filename when I loop trough these files in BASH. How do I achieve this in Bash?

[SNPsaurus]

You want to split the string on a "." delimiter and then keep the first two parts. Or use ".fastq.sam.bam" as a delimiter, I suppose!

https://www.tutorialkart.com/bash-shell-scripting/bash-split-string/

[ungsik]

Refer to https://unix.stackexchange.com/quest...ck-of-variable

An example for changing extension from fastq.sam.bam to txt.

for file in *.fastq.sam.bam
do
mv ${file%.fastq.sam.bam} ${file%.fastq.sam.bam}.txt
done

[pmiguel]

Refer to https://unix.stackexchange.com/quest...ck-of-variable

An example for changing extension from fastq.sam.bam to txt.

for file in *.fastq.sam.bam
do
mv ${file%.fastq.sam.bam} ${file%.fastq.sam.bam}.txt
done

Don't you mean:

for file in *.fastq.sam.bam
do
mv $file ${file%.fastq.sam.bam}.txt
done

--
Phillip

[pmiguel]

I have many files named like this:

lib01.GFBAG_UHAU.fastq.sam.bam
lib02.ABABAB_ZU.fastq.sam.bam
lib03.ZGAZG_IAUDH.fastq.sam.bam

Many parts of the filenames are thus variable in length, although they are connected through the same type of punctuation (. or _).
What I want to achieve is to remove the part .fastq.sam.bam from a filename when I loop trough these files in BASH. How do I achieve this in Bash?

Using BASH parameter expansion:

for i in *.fastq.sam.bam; do mv $i ${i%.fastq.sam.bam}; done;

Which is pretty fun, the "%" more-or-less meaning "clip what follows from the the very end of the value stored in variable $i." "#" does the analogous thing, but clips from the very front.

But "%%" does a "greedy" removal of whatever follows it. So:

i=lib01.GFBAG_UHAU.fastq.sam.bam.fastq.sam.bam.fastq.sam.bam
echo ${i%.fastq.sam.bam*}

will produce:

lib01.GFBAG_UHAU.fastq.sam.bam.fastq.sam.bam

whereas:

i=lib01.GFBAG_UHAU.fastq.sam.bam.fastq.sam.bam.fastq.sam.bam
echo ${i%%.fastq.sam.bam*}

will produce:

lib01.GFBAG_UHAU

If you can run Perl, then finding the "rename.pl" script might be less arcane than deploying you BASH powers.

rename.pl 's/.fastq.sam.bam$//' *.fastq.sam.bam

Find rename.pl here:

https://stackoverflow.org/wiki/Rename.pl

--
Phillip

[pmiguel]

I have many files named like this:

lib01.GFBAG_UHAU.fastq.sam.bam
lib02.ABABAB_ZU.fastq.sam.bam
lib03.ZGAZG_IAUDH.fastq.sam.bam

Many parts of the filenames are thus variable in length, although they are connected through the same type of punctuation (. or _).
What I want to achieve is to remove the part .fastq.sam.bam from a filename when I loop trough these files in BASH. How do I achieve this in Bash?

Using BASH parameter expansion:

for i in *.fastq.sam.bam; do mv $i ${i%.fastq.sam.bam}; done;

Which is pretty fun, the "%" more-or-less meaning "clip what follows from the the very end of the value stored in variable $i." "#" does the analogous thing, but clips from the very front.

But "%%" does a "greedy" removal of whatever follows it. So:

i=lib01.GFBAG_UHAU.fastq.sam.bam.fastq.sam.bam.fastq.sam.bam
echo ${i%.fastq.sam.bam*}

will produce:

lib01.GFBAG_UHAU.fastq.sam.bam.fastq.sam.bam

whereas:

i=lib01.GFBAG_UHAU.fastq.sam.bam.fastq.sam.bam.fastq.sam.bam
echo ${i%%.fastq.sam.bam*}

will produce:

lib01.GFBAG_UHAU

If you can run Perl, then finding the "rename.pl" script might be less arcane than deploying you BASH powers.

rename.pl 's/.fastq.sam.bam$//' *.fastq.sam.bam

Find rename.pl here:

https://stackoverflow.org/wiki/Rename.pl

--
Phillip

[malcook]

A range of options exists for munging the pathnames

The approach I would use might well depend on what else I going to do in the loop.

FWIW:

[basename](https://linux.die.net/man/1/basename) can be used to remove a suffix of a filename.

[Shell Parameter Expansion](https://www.gnu.org/software/bash/ma...Expansion.html) can be used to strip or replace either suffixes or prefixes of pathnames stored in variables.

[GNU parallel](https://www.gnu.org/software/parallel/) can be used in effect to replace your bash looping construct, and has simple syntax for to refer to the basename of a file or directory, including `{=perl expression=}` to munge the pathname any way you like. It has MANY great features and is well worth exploring and being in your toolbelt.

[rename](https://www.computerhope.com/unix/rename.htm) is very useful for batch renaming of files using regular expressions (if that is all you need to do).