Answers.Body: <p>Just execute the following immediately above the directories of interest, (<strong>post edited</strong> to include OPs &quot;constant term&quot;)</p>
  <pre><code>for d in *; do 
    mv &quot;<span class="math-container">$d"/ragtag.scaffold.fasta 
   "$</span>d/${d/000mergedCluster_/}_ragtag.scaffold.fasta&quot;;
  done
  </code></pre>
  <p>The key thing I assumed is that the directory name comprises a &quot;constant term&quot; and is suffixed by a &quot;variable term&quot;.</p>
  <p>Just to note the <code>$d</code> here is directory not file name - because that is constant in each directory.</p>
  <hr />
  <p>Comments...</p>
  <pre><code><span class="math-container">$d/$</span>{d/000mergedCluster_/}
  </code></pre>
  <p>The key part of the code is above.</p>
  <p>What its doing is saying from the variable <code>$d</code> delete the term <code>000mergedCluster_</code> (or whatever the &quot;constant term&quot; is)</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-17T21:55:09.917Z
Answers.Text: 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?
Answers.UserDisplayName: rimo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-17T21:59:04.490Z
Answers.Text: @rimo What is your "constant term" in the directory name?
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-17T22:00:05.923Z
Answers.Text: The whole name is something like "000mergedCluster_1234" so the constant term is "000mergedCluster_" and the variable term is "1234"
Answers.UserDisplayName: rimo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-17T22:04:49.213Z
Answers.Text: @rimo Can you try it now? If you copy and pasted the edited code that should work
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-17T22:06:54.387Z
Answers.Text: 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!
Answers.UserDisplayName: rimo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-18T00:18:49.687Z
Answers.Text: The asterisk wildcard by itself will match all files and directories (except dot files/folders). There's no guarantee that `$d` is actually a directory. Better to use a more specific pattern, for example: `for d in 000mergedCluster_*`.
Answers.UserDisplayName: Steve
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-18T01:25:59.860Z
Answers.Text: @Steve agreed. That should have been updated, but at the time the directory name was not known, however `for d in *_*` would have been better.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-17T21:45:54.757Z
Answers.LastActivityDate: 2023-01-18T12:14:58.090Z
Answers.LastEditDate: 2023-01-18T12:14:58.090Z
Answers.UserDisplayName: M__
Answers.Body: <p>Assuming the output is only a list of directories and each directory includes a file called &quot;ragtag.scaffold.fasta&quot;, you could use <a href="https://www.gnu.org/software/bash/manual/html_node/Brace-Expansion.html" rel="nofollow noreferrer">brace expansion</a> to generate the SOURCE and DEST strings:</p>
  <pre><code>for i in directoryName_* ; do
      echo mv &quot;${i}&quot;/{,&quot;${i#directoryName_}&quot;_}ragtag.scaffold.fasta
  done
  </code></pre>
  <p>But the above will only work using Bash and Zsh, and maybe some other shells. Without Bash/Zsh, just use:</p>
  <pre><code>fasta=&quot;ragtag.scaffold.fasta&quot;
  for i in directoryName_* ; do
      echo mv &quot;${i}/${fasta}&quot; &quot;${i}/${i#directoryName_}_${fasta}&quot;
  done
  </code></pre>
  <p>Remove the <code>echo</code> to perform the rename.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-18T00:06:52.680Z
Answers.LastActivityDate: 2023-01-18T00:06:52.680Z
Answers.UserDisplayName: Steve
Answers.Body: <p>If you want to use Perl:</p>
  <pre class="lang-pl prettyprint-override"><code>#!/usr/bin/perl
  use 5.030;
  use warnings;
  
  use File::Find::Rule qw( );
  
  for my <span class="math-container">$file (File::Find::Rule-&gt;name("ragtag.scaffold.fasta")-&gt;in(".")){
    my $newfile = $file;
    $newfile =~ s{(.+_(\d+)/)(.+.fasta)}{$1$2_$</span>3};
  
    if (-e <span class="math-container">$newfile) {
      warn "can't rename $file to $newfile: $newfile exists\n";
    }elsif (rename $</span>file, <span class="math-container">$newfile) {
      # do nothing
    }else{
      warn "rename $file to $newfile failed: $</span>!\n&quot;;
    }
  }
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-19T04:16:59.123Z
Answers.LastActivityDate: 2023-01-19T04:35:12.333Z
Answers.LastEditDate: 2023-01-19T04:35:12.333Z
Answers.UserDisplayName: Supertech
Answers.Body: <p>Perl one-liner:</p>
  <pre class="lang-sh prettyprint-override"><code>ls */filename | perl -lane 'print &quot;mv $1/$3 $1/$2_$3&quot; if /(\S+_([^\/_\s]+))\/(\S+)/'
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-21T04:19:41.587Z
Answers.LastActivityDate: 2023-01-21T04:19:41.587Z
Answers.UserDisplayName: user172818
Body: <p>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 &quot;ragtag.scaffold.fasta&quot;</p>
  <p>I would like to go through each file and rename it like so:</p>
  <pre><code>Original Path with File name:
  directoryName_ID/ragtag.scaffold.fasta
  
  Changed File name:
  directoryName_ID/ID_ragtag.scaffold.fasta
  </code></pre>
  <p>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 &quot;_&quot; in the directory name and to use that to rename my fasta file?</p>
  <p>Here is what I have tried so far:</p>
  <pre><code>for filename in ./directory*/ragtag.scaffold.fasta; do 
      mv filename ${./directory%*_*}_ragtag.scaffold.fasta; 
  done
  </code></pre>
  <p>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!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-18T20:38:24.027Z
Comments.Text: What operating system are you running on?
Comments.UserDisplayName: gringer
Tags: <fasta><bash><command-line><ragtag><for-loop>
Title: How to rename a file based on a directory name?
ThreadText: # How to rename a file based on a directory name?
  
  (Asked by: username_0 on 2023-01-17)
  
  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!
  
  **Tags:** fasta, bash, command-line, ragtag, for-loop
  
  > **Comments:**
  > **username_1**: What operating system are you running on?  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_2 on 2023-01-17. Score: 3 | Accepted answer
  
  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)
  
  > **Comments:**
  > **username_0**: 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?  
  > **username_2**: @username_0 What is your "constant term" in the directory name?  
  > **username_0**: The whole name is something like "000mergedCluster_1234" so the constant term is "000mergedCluster_" and the variable term is "1234"  
  > **username_2**: @username_0 Can you try it now? If you copy and pasted the edited code that should work  
  > **username_0**: 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!  
  > **username_3**: 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_*`.  
  > **username_2**: @username_3 agreed. That should have been updated, but at the time the directory name was not known, however `for d in *_*` would have been better.  
  
  ---
  
  ### Answer by username_3 on 2023-01-18. Score: 3
  
  Assuming the output is only a list of directories and each directory includes a file called "ragtag.scaffold.fasta", you could use [brace expansion](https://www.gnu.org/software/bash/manual/html_node/Brace-Expansion.html) 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.
  
  
  ---
  
  ### Answer by username_4 on 2023-01-19. Score: 1
  
  If you want to use Perl:
  
  ```pl
  #!/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";
    }
  }
  
  ```
  
  
  ---
  
  ### Answer by username_5 on 2023-01-21. Score: 1
  
  Perl one-liner:
  
  ```sh
  ls */filename | perl -lane 'print "mv $1/$3 $1/$2_$3" if /(\S+_([^\/_\s]+))\/(\S+)/'
  
  ```
  
  
  ---
  
  