This question already has answers here:
How to rename with prefix/suffix?
(10 answers)
Closed 7 years ago.
there are 30 files named like this:
sample_kmer_41_2.lib1.bowtie.file1.27.faabyss_sample
I need the output to be:
abyss_sample_kmer_41_2.lib1.bowtie.file1.27.fa
I don't know how to do this, I've already screwed the names up a lot. thanks for any help.
Use the rename utility:
rename 's/(.*)\.fa(.*)_sample$/$2_$1/' *
rename is part of the perl package and is installed by default on debian-like systems. There is a different and incompatible rename utility that is provided as part of the util-linux packages.
If you have the Perl-based prename (possibly named rename) command, then:
prename 's/(.*)abyss_sample$/abyss_$1/' sample_kmer_*
The exact regex to use depends on how the names have been damaged. This should work for the example name given; it may need tweaking to work with other names.
You could use a for loop. Since I'm always nervous about this stuff I'd recommend doing an echo first to make sure everything looks groovy...
#!/bin/bash
for FILE in sample_kmer_41_2*abyss_sample ; do
NEWNAME=`echo $FILE | sed -e 's/abyss_sample//'`
echo mv $FILE $NEWNAME
done
Provided that doesn't need tweaking, you can remove the echo or make modifications as necessary.
Related
I am using an application that creates a text file on a Linux server. I then have the ability to execute a shell script (BASH 3.2.57) in which I need to convert the text file from Unix line endings to DOS and also change the extension of the file from .txt to .log.
I currently have a sed based command to do this. This command is rewritten by the application at run time to point to the specific folder and file name, in this example where you see ABC (all capital 3 letters in all my examples are a variable that can be any 3 letters).
pushd /rootfolder/parentfolder/ABC/
sed 's/$/\r/' prABC.txt > prABC.log
popd
The problem with this is that if a user runs the application for 2 different groups, say ABC and DEF at nearly the same time, the script will get overwritten with the DEF variables before ABC had a chance to fire off and do its thing with the file. Additionally the .txt is left in the folder regardless and I would like that to be removed.
A friend of mine came up with the following code that seems to work if its determined to be our best solution, but I would think and hope we have a cleaner more dynamic way to do this. Also this current method requires that when my user decides to add a GHI directory and file I now have to update the code, which i can program my application to do for me but i don't want this script to have to be rewritten every time the application wants to use it.
pushd /rootfolder/parentfolder/ABC
if [[ -f prABC.txt ]]
then
sed 's/$/\r/' prABC.txt > prABC.log
rm prABC.txt
fi
popd
pushd /rootfolder/parentfolder/DEF
if [[ -f prABC.txt ]]
then
sed 's/$/\r/' prABC.txt > prABC.log
rm prABC.txt
fi
popd
I would like to call this script at anytime from my application and it find any file named pr*.txt below the /rootfolder/parentfolder/ directory (if that has to include the parentfolder in its search that won't be a problem) and convert the line endings from LF to CRLF and change the extension of the file from .txt to .log.
I've done a ton of searching and have found near solutions for this but not exactly what I need and I want to be sure it's as safe as possible (issues with using "find with for". I don't know what utilities are installed on this build so i would like to keep it as basic/supportable as possible Thanks in advance :)
You should almost never need pushd and popd in scripts. In fact, you rarely need cd, either.
#!/bin/bash
for d in /rootfolder/parentfolder/ABC /rootfolder/parentfolder/DEF
do
if [[ -f "$d/prABC.txt" ]]
then
sed 's/$/\r/' "$d/prABC.txt" > "$d/prABC.log" &&
rm "$d/prABC.txt"
fi
done
Recall that a && b is shorthand for
if a; then
b
fi
In other words, if sed fails (because the source file can't be read, or the destination can't be written) we don't rm the source file. There should be an error message already so we don't add another one.
Not only is this more succinct, it is also easier to change if you decide that the old file should be renamed instead of removed, or you want to filter out all lines which contain "beef" in the sed script. Generally you should avoid repeated code; see also the DRY principle on Wikipedia.
Something is seriously wrong somewhere if you require DOS line endings in your files on Unix.
I want to replace double spaces with one space in the filenames of a lot of photos. These photos are located in directory /foto and it's subfolders. How to do this? For example "photo 1.jpg" needs to become "photo 1.jpg"
The best way is to use commandline, because it's on CloudLinux server. (and it is over 50GB of photos). I searched here on Stackoverflow, also Google to find the command I need. I guess rename is the one to use, or mv.
The only things I found were commands about replacing space and replacing other symbols, but not about double (multiple) spaces.
find -iname \*.* | rename -v "s/\s{2}/ /g"
This is the final command which helped me out. I used perl rename, see answer by Gilles
Use this, using Perl's rename :
rename 's/\s{2}/ /g' files*
Remove -n switch when the output looks good.
There are other tools with the same name which may or may not be able to do this, so be careful.
If you run the following command (GNU)
$ file "$(readlink -f "$(type -p rename)")"
and you have a result that contains Perl script, ASCII text executable and not containing ELF, then this seems to be the right tool =)
If not, to make it the default (usually already the case) on Debian and derivative like Ubuntu :
$ sudo update-alternatives --set rename /path/to/rename
Replace /path/to/rename to the path of your perl rename executable.
If you don't have this command, search your package manager to install it or do it manually (no deps...)
This tool was originally written by Larry Wall, the Perl's dad.
There are multiple files in /opt/dir/ABC/ named allfile_123-abc allfile_123-def allfile_123-ghi allfile_123-xxx.
I need the files to be named new_name-abc.pgp new_name-def.pgp new_name-ghi.pgp new_name-xxx.pgp and then moved to /usr/tst/output
for file in /opt/dir/ABC/allfile_123* ;
do mv $file /usr/tst/output/"$file.pgp";
rename allfile_123 new_name /usr/tst/output/*.pgp ; done
I know the above doesn't work because $file = /opt/dir/ABC/allfile_123*. Is it possible to make this work, or is it a different command instead of 'for loop'?
This is for the Autosys application in which the jil contains a command to pass to the command line of a linux server running bash.
I could only find versions of each part of my question but not altogether and I was hoping to keep it on the command line of this jil. Unless a script is absolutely necessary.
No need for the loop, you can do this with just rename and mv:
rename -v 's/$/.pgp/' /opt/dir/ABC/allfile_123*
rename -v s/allfile_123/new_name/ /opt/dir/ABC/allfile_123*
mv /opt/dir/ABC/new_name* /usr/tst/output/
But I'm not sure the rename you are using is the same as mine.
However,
since the replacement you want to perform is fairly simple,
it's easy to do in pure Bash:
for file in /opt/dir/ABC/allfile_123*; do
newname=new_name${file##*allfile_123}.gpg
mv "$file" /usr/tst/output/"$newname"
done
If you want to write it on a single line:
for file in /opt/dir/ABC/allfile_123*; do newname=new_name${file##*allfile_123}.gpg; mv "$file" /usr/tst/output/"$newname"; done
This question already has answers here:
Rename multiple files based on pattern in Unix
(24 answers)
Closed 2 years ago.
I have a folder containing a sequence of files whose names bear the form filename-white.png. e.g.
images
arrow-down-white.png
arrow-down-right-white.png
...
bullets-white.png
...
...
video-white.png
I want to strip out the -white bit so the names are simply filename.png. I have played around, dry run with -n, with the Linux rename command. However, my knowledge of regexes is rather limited so I have been unable to find the right way to do this.
If you are in the directory above images, the command is
rename "s/-white.png/.png/" images/*
If your current directory is images, then run rename "s/-white.png/.png/" ./* instead. To do a dry run, just attach a -n like you said:
rename -n "s/-white.png/.png/" images/*
or
rename -n "s/-white.png/.png/" ./*
I have a RedHat linux box and I had written a script in the past to move files from one location to another with a specific text in the body of the file.
I typically only write scripts once a year so every year I forget more and more... That being said,
Last year I wrote this script and used it and it worked.
For some reason, I can not get it to work today and I know it's a simple issue and I shouldn't even be asking for help but for some reason I'm just not looking at it correctly today.
Here is the script.
ls -1 /var/text.old | while read file
do
grep -q "to.move" $file && mv $file /var/text.old/TBD
done
I'm listing all the files inside the /var/text.old directory.
I'm reading each file
then I'm grep'ing for "to.move" and holing the results
then I'm moving the resulting found files to the folder /var/text.old/TBD
I am an admin and I have rights to the above files and folders.
I can see the data in each file
I can mv them manually
I have use pwd to grab the correct spelling of the directory.
If anyone can just help me to see what the heck I'm missing here that would really make my day.
Thanks in advance.
UPDATE:
The files I need to move do not have Whitespaces.
The Error I'm getting is as follows:
grep: 9829563.msg: No such file or directory
NOTE: the file "982953.msg" is one of the files I need to move.
Also note: I'm getting this error for every file in the directory that I'm listing.
You didn't post any error, but I'm gonna take a guess and say that you have a filename with a space or special shell character.
Let's say you have 3 files, and ls -1 gives us:
hello
world
hey there
Now, while splits on the value of the special $IFS variable, which is set to <space><tab><newline> by default.
So instead of looping of 3 values like you expect (hello, world, and hey there), you loop over 4 values (hello, world, hey, and there).
To fix this, we can do 2 things:
Set IFS to only a newline:
IFS="
"
ls -1 /var/text.old | while read file
...
In general, I like setting IFS to a newline at the start of the script, since I consider this to be slightly "safer", but opinions on this probably vary.
But much better is to not parse the output of ls, and use for:
for file in /var/text.old/*`; do
This won't fork any external processes (piping to ls to while starts 2), and behaves "less surprising" in other ways. See here for some examples.
The second problem is that you're not quoting $file. You should always quote pathnames with double quoted: "$file" for the same reasons. If $file has a space (or a special shell character, such as *, the meaning of your command changes:
file=hey\ *
mv $file /var/text.old/TBD
Becomes:
mv hey * /var/text.old/TBD
Which is obviously very different from what you intended! What you intended was:
mv "hey *" /var/text.old/TBD