How to rename a file based on a directory name?

Question

I have a lot of FASTA files that I recently scaffolded with RagTag. The output of RagTag includes a directory for each sample and the corresponding FASTA file written as "ragtag.scaffold.fasta"

I would like to go through each file and rename it like so:

Original Path with File name:
directoryName_ID/ragtag.scaffold.fasta
Changed File name:
directoryName_ID/ID_ragtag.scaffold.fasta

As you can see, the directory name includes the ID number I would like to use to rename the fasta file with (along with an underscore to space it out). Is there a way to loop through all of the directories, using that last number after the "_" in the directory name and to use that to rename my fasta file?

Here is what I have tried so far:

for filename in ./directory*/ragtag.scaffold.fasta; do 
    mv filename ${./directory%*_*}_ragtag.scaffold.fasta; 
done

It doesn't work at all but I know I need to use mv to rename the filename. However, when it comes to referencing the directory name the file is located in I get lost. I also have a .txt file that contains a list of IDs if that might be easier to reference. I'm still kinda new to the command line so if anyone could help that would be greatly appreciated!

What operating system are you running on? – gringer Jan 18 '23 at 20:38 — gringer, Jan 18 '23 at 20:38

score 3 · Accepted Answer · edited Jan 18 '23 at 12:14

3

Just execute the following immediately above the directories of interest, (post edited to include OPs "constant term")

for d in *; do 
  mv "$d"/ragtag.scaffold.fasta 
 "$d/${d/000mergedCluster_/}_ragtag.scaffold.fasta";
done

The key thing I assumed is that the directory name comprises a "constant term" and is suffixed by a "variable term".

Just to note the $d here is directory not file name - because that is constant in each directory.

Comments...

$d/${d/000mergedCluster_/}

The key part of the code is above.

What its doing is saying from the variable $d delete the term 000mergedCluster_ (or whatever the "constant term" is)

edited Jan 18 '23 at 12:14

terdon

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answered Jan 17 '23 at 21:45

M__

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Thank you this works great! Only thing is that it includes the "constant term" in the new renamed file...is there a way to change it so only the "variable term" (whats after the _ in the original file name) is added to the file name? – rimo Jan 17 '23 at 21:55
@rimo What is your "constant term" in the directory name? – M__ Jan 17 '23 at 21:59
1

The whole name is something like "000mergedCluster_1234" so the constant term is "000mergedCluster_" and the variable term is "1234" – rimo Jan 17 '23 at 22:00
@rimo Can you try it now? If you copy and pasted the edited code that should work – M__ Jan 17 '23 at 22:04
1

She's perfect! Sorry that was silly of me but I completely understand what this command is doing now. Thank you so much for your help!! This works great! – rimo Jan 17 '23 at 22:06
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The asterisk wildcard by itself will match all files and directories (except dot files/folders). There's no guarantee that $d is actually a directory. Better to use a more specific pattern, for example: for d in 000mergedCluster_*. – Steve Jan 18 '23 at 00:18
@Steve agreed. That should have been updated, but at the time the directory name was not known, however for d in *_* would have been better. – M__ Jan 18 '23 at 01:25

score 3 · Answer 2 · answered Jan 18 '23 at 00:06

Assuming the output is only a list of directories and each directory includes a file called "ragtag.scaffold.fasta", you could use brace expansion to generate the SOURCE and DEST strings:

for i in directoryName_* ; do
    echo mv "${i}"/{,"${i#directoryName_}"_}ragtag.scaffold.fasta
done

But the above will only work using Bash and Zsh, and maybe some other shells. Without Bash/Zsh, just use:

fasta="ragtag.scaffold.fasta"
for i in directoryName_* ; do
    echo mv "${i}/${fasta}" "${i}/${i#directoryName_}_${fasta}"
done

Remove the echo to perform the rename.

Supertech · Answer 3 · 2023-01-19T04:35:12.333

If you want to use Perl:

#!/usr/bin/perl
use 5.030;
use warnings;
use File::Find::Rule qw( );
for my $file (File::Find::Rule->name("ragtag.scaffold.fasta")->in(".")){
  my $newfile = $file;
  $newfile =~ s{(.+(\d+)/)(.+.fasta)}{$1$2$3};
if (-e $newfile) {
    warn "can't rename $file to $newfile: $newfile exists\n";
  }elsif (rename $file, $newfile) {
    # do nothing
  }else{
    warn "rename $file to $newfile failed: $!\n";
  }
}

score 1 · Answer 4 · answered Jan 21 '23 at 04:19

1

Perl one-liner:

ls */filename | perl -lane 'print "mv $1/$3 $1/$2_$3" if /(\S+_([^\/_\s]+))\/(\S+)/'

answered Jan 21 '23 at 04:19

user172818

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How to rename a file based on a directory name?

4 Answers4