I would like to modify the name of several files in a folder. The name are in this format:
Name_name_name_name_XXXX.fa
I would like:
XXXX_Name_name_name_name.fa
I tired using
for f in *.fa; do mv "${f/.fa/Name_name_name_name.fa}";done
output Name_name_name_name_XXXX_Name_name_name_name.fa
and then
for f in *.fa; do mv "${f/Name_name_name_name_//}"; done
to remove the 4 name_name. but it didnt work.
Any idea how to do it?
You can use sed:
for f in *.fa; do
mv "$f" $(sed -E 's/^(.+)_([^.]+)\./\2_\1./' <<< "$f")
done
sed command uses 2 capture groups. 1st group contains string before last underscore and 2nd group contains XXXX part (part between last _` and dot).
Try this using perl's rename in just one command using regex capture groups:
rename -n 's/(.*?)_([^_]+)\.fa$/$2_$1/' *.fa
(remove -n switch when your tests are OK)
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 like
.../rename: 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's rename command.
If you don't have this command, search your package manager to install it or do it manually
Last but not least, this tool was originally written by Larry Wall, the Perl's dad.
Related
I want to rename files names by substituting all the characters starting from "_ " followed by eight capital letter and keep only the extension.
4585_10_148_H2A119Ub_GTCTGTCA_S51_mcdf_mdup_ngsFlt.fm
4585_10_148_H3K27me3_TCTTCACA_S51_mcdf_mdup_ngsFlt.fm
4585_27_128_Bap1_Bethyl_ACAGATTC_S61_mcdf_mdup_ngsFlt.fw
4585_32_148_1_INPUT_previous_AGAGTCAA_S72_mcdf_mdup_ngsFlt.bw
expected output
4585_10_148_H2A119Ub.fm
4585_10_148_H3K27me3.fm
4585_27_128_Bap1_Bethyl.fm
4585_32_148_1_INPUT_previous.fm
Try this:
for f in *; do
target=$(echo "${f}" | sed -E 's/_[[:upper:]]{8}.*\././')
mv "${f}" "${target}"
done
The key thing is the -E argument to sed, since it enables expanded regular expressions.
You can also use rename (a.k.a. prename or Perl rename) like this:
rename --dry-run 's|_[[:upper:]]{8}.*\.|.|' *
Sample Output
'4585_10_148_H2A119Ub_GTCTGTCA_S51_mcdf_mdup_ngsFlt.fm' would be renamed to '4585_10_148_H2A119Ub.fm'
'4585_32_148_1_INPUT_previous_AGAGTCAA_S72_mcdf_mdup_ngsFlt.bw' would be renamed to '4585_32_148_1_INPUT_previous.bw'
Remove the --dry-run and run again for real, if the output looks good.
This has several added benefits:
that it will warn and avoid any conflicts if two files rename to the same thing,
that it can rename across directories, creating any necessary intermediate directories on the way,
that you can do a dry run first to test it,
that you can use arbitrarily complex Perl code to specify the new name.
On a Mac, install it with homebrew using:
brew install rename
You may try this.
for i in *.fm; do mv $i $(echo $i | sed 's/_GTCTGTCA_S51_mcdf_mdup_ngsFlt//g'); done;
for i in *.fm; do mv $i $(echo $i | sed 's/_TCTTCACA_S51_mcdf_mdup_ngsFlt//g'); done;
Using wget, a webpage is downloaded as a .txt file. This file saved is named using part of the url of the webpage, eg. wget http://www.example.com/page/12345/ -O 12345.txt, for convenience.
I am running commands from a shell script .sh file, as it can execute multiple commands, one line at time, eg.
After a file is downloaded, I use sed to parse for text / characters I want to keep. Part of the text I want includes blah blah Product ID a5678.
What I want is to use sed to find a5678 and use this to rename the file 12345.txt to a5678.txt.
# script.sh
wget http://www.example.com/page/12345/ -O 12345.txt
sed -i '' 's/pattern/replace/g' 12345.txt
sed command to find a5678 # in line blah blah Product ID a5678
some more sed commands
mv 12345.txt a5678.txt (or use a variable $var.txt)?
How do I do this?
I may also want to use this same ID a5678 and create a folder with the same name a5678. Hence the .txt file is inside the folder like so /a5678/a5678.txt.
mkdir a5678 (or mkdir $var)? && cd a5678
I've searched for answers for half a day, but can't find any. The closest I found is
Find instance of word in files and change it to the filename but it is the exact opposite of what I want. I've also thought about using variables eg. https://askubuntu.com/questions/76808/how-do-i-use-variables-in-a-sed-command but I don't know how to save the found characters as a variable.
Very much look forward to some help! Thank you! I am on a Mac running Sierra.
Trying to minimize, so fit this into your logic.
in=12345.txt
out=$( grep ' Product ID ' $in | sed 's/.* Product ID \([^ ]*\) .*/\1/' )
mkdir -p $out
mv $in $out/$out.txt
Thank you all! With your inspiration, I solved my problem by (without using grep):
in=12345
out=$(sed -n '/pattern/ s/.*ID *//p' $in.txt)
mv $in.txt $out.txt
cd ..
mv $in $out
I have a bunch of files in Unix Directory :
test_XXXXX.txt
best_YYY.txt
nest_ZZZZZZZZZ.txt
I need to rename these files as
test.txt
best.txt
nest.txt
I am using Ksh on AIX .Please let me know how i can accomplish the above using a Single command .
Thanks,
In this case, it seems you have an _ to start every section you want to remove. If that's the case, then this ought to work:
for f in *.txt
do
g="${f%%_*}.txt"
echo mv "${f}" "${g}"
done
Remove the echo if the output seems correct, or replace the last line with done | ksh.
If the files aren't all .txt files, this is a little more general:
for f in *
do
ext="${f##*.}"
g="${f%%_*}.${ext}"
echo mv "${f}" "${g}"
done
If this is a one time (or not very often) occasion, I would create a script with
$ ls > rename.sh
$ vi rename.sh
:%s/\(.*\)/mv \1 \1/
(edit manually to remove all the XXXXX from the second file names)
:x
$ source rename.sh
If this need occurs frequently, I would need more insight into what XXXXX, YYY, and ZZZZZZZZZZZ are.
Addendum
Modify this to your liking:
ls | sed "{s/\(.*\)\(............\)\.txt$/mv \1\2.txt \1.txt/}" | sh
It transforms filenames by omitting 12 characters before .txt and passing the resulting mv command to a shell.
Beware: If there are non-matching filenames, it executes the filename—and not a mv command. I omitted a way to select only matching filenames.
I have a directory full of files with one extension (.txt in this case) that I want to automatically convert to another extension (.md).
Is there an easy terminal one-liner I can use to convert all of the files in this directory to a different file extension?
Or do I need to write a script with a regular expression?
You could use something like this:
for old in *.txt; do mv $old `basename $old .txt`.md; done
Make a copy first!
Alternatively, you could install the ren (rename) utility
brew install ren
ren '*.txt' '#1.md'
If you want to rename files with prefix or suffix in file names
ren 'prefix_*.txt' 'prefix_#1.md'
Terminal is not necessary for this... Just highlight all of the files you want to rename. Right click and select "Rename ## items" and just type ".txt" into to the "Find:" box and ".md" into the "Replace with:" box.
The preferred Unix way to do this (yes, OS X is based on Unix) is:
ls | sed 's/^\(.*\)\.txt$/mv "\1.txt" "\1.md"/' | sh
Why looping with for if ls by design loops through the whole list of filenames? You've got pipes, use them. You can create/modify not only output using commands, but also commands (right, that is commands created by a command, which is what Brian Kernighan, one of the inventors of Unix, liked most on Unix), so let's take a look what the ls and the sed produces by removing the pipe to sh:
$ ls | sed 's/^\(.*\)\.txt$/mv "\1.txt" "\1.md"/'
mv "firstfile.txt" "firstfile.md"
mv "second file.txt" "second file.md"
$
As you can see, it is not only an one-liner, but a complete script, which furthermore works by creating another script as output. So let's just feed the script produced by the one-liner script to sh, which is the script interpreter of OS X. Of course it works even for filenames with spaces in it.
BTW: Every time you type something in Terminal you create a script, even if it is only a single command with one word like ls or date etc. Everything running in a Unix shell is always a script/program, which is just some ASCII-based stream (in this case an instruction stream opposed to a data stream).
To see the actual commands being executed by sh, just add an -x option after sh, which turns on debugging output in the shell, so you will see every mv command being executed with the actual arguments passed by the sed editor script (yeah, another script inside the script :-) ).
However, if you like complexity, you can even use awk and if you like to install other programs to just do basic work, there is ren. I know even people who would prefer to write a 50-lines or so perl script for this simple every-day task.
Maybe it's easier in finder to rename files, but if connected remotely to a Mac (e.g. via ssh), using finder is not possible at all. That's why cmd line still is very useful.
Based on the selected and most accurate answer above, here's a bash function for reusability:
function change_all_extensions() {
for old in *."$1"; do mv $old `basename $old ."$1"`."$2"; done
}
Usage:
$ change_all_extensions txt md
(I couldn't figure out how to get clean code formatting in a comment on that answer.)
No need to write a script for it just hit this command
find ./ -name "*.txt" | xargs -I '{}' basename '{}' | sed 's/\.txt//' | xargs -I '{}' mv '{}.txt' '{}.md'
You do not need a terminal for this one; here is a sample demonstration in MacOS Big Sur.
Select all the files, right-click and select "rename..."
Add the existing file extension in "Find" and the extension you want to replace with "Replace with".
And done!
I had a similar problem where files were named .gifx.gif at the end and this worked in OS X to remove the last .gif:
for old in *.gifx.gif; do
mv $(echo "$old") $(echo "$old" | sed 's/x.gif//');
done
cd $YOUR_DIR
ls *.txt > abc
mkdir target // say i want to move it to another directory target in this case
while read line
do
file=$(echo $line |awk -F. '{ print $1 }')
cp $line target/$file.md // depends if u want to move(mv) or copy(cp)
done < abc
list=ls
for file in $list
do
newf=echo $file|cut -f1 -d'.'
echo "The newf is $newf"
mv $file $newf.jpg
done
Objective
Change these filenames:
F00001-0708-RG-biasliuyda
F00001-0708-CS-akgdlaul
F00001-0708-VF-hioulgigl
to these filenames:
F0001-0708-RG-biasliuyda
F0001-0708-CS-akgdlaul
F0001-0708-VF-hioulgigl
Shell Code
To test:
ls F00001-0708-*|sed 's/\(.\).\(.*\)/mv & \1\2/'
To perform:
ls F00001-0708-*|sed 's/\(.\).\(.*\)/mv & \1\2/' | sh
My Question
I don't understand the sed code. I understand what the substitution
command
$ sed 's/something/mv'
means. And I understand regular expressions somewhat. But I don't
understand what's happening here:
\(.\).\(.*\)
or here:
& \1\2/
The former, to me, just looks like it means: "a single character,
followed by a single character, followed by any length sequence of a
single character"--but surely there's more to it than that. As far as
the latter part:
& \1\2/
I have no idea.
First, I should say that the easiest way to do this is to use the
prename or rename commands.
On Ubuntu, OSX (Homebrew package rename, MacPorts package p5-file-rename), or other systems with perl rename (prename):
rename s/0000/000/ F0000*
or on systems with rename from util-linux-ng, such as RHEL:
rename 0000 000 F0000*
That's a lot more understandable than the equivalent sed command.
But as for understanding the sed command, the sed manpage is helpful. If
you run man sed and search for & (using the / command to search),
you'll find it's a special character in s/foo/bar/ replacements.
s/regexp/replacement/
Attempt to match regexp against the pattern space. If success‐
ful, replace that portion matched with replacement. The
replacement may contain the special character & to refer to that
portion of the pattern space which matched, and the special
escapes \1 through \9 to refer to the corresponding matching
sub-expressions in the regexp.
Therefore, \(.\) matches the first character, which can be referenced by \1.
Then . matches the next character, which is always 0.
Then \(.*\) matches the rest of the filename, which can be referenced by \2.
The replacement string puts it all together using & (the original
filename) and \1\2 which is every part of the filename except the 2nd
character, which was a 0.
This is a pretty cryptic way to do this, IMHO. If for
some reason the rename command was not available and you wanted to use
sed to do the rename (or perhaps you were doing something too complex
for rename?), being more explicit in your regex would make it much
more readable. Perhaps something like:
ls F00001-0708-*|sed 's/F0000\(.*\)/mv & F000\1/' | sh
Being able to see what's actually changing in the
s/search/replacement/ makes it much more readable. Also it won't keep
sucking characters out of your filename if you accidentally run it
twice or something.
you've had your sed explanation, now you can use just the shell, no need external commands
for file in F0000*
do
echo mv "$file" "${file/#F0000/F000}"
# ${file/#F0000/F000} means replace the pattern that starts at beginning of string
done
I wrote a small post with examples on batch renaming using sed couple of years ago:
http://www.guyrutenberg.com/2009/01/12/batch-renaming-using-sed/
For example:
for i in *; do
mv "$i" "`echo $i | sed "s/regex/replace_text/"`";
done
If the regex contains groups (e.g. \(subregex\) then you can use them in the replacement text as \1\,\2 etc.
The easiest way would be:
for i in F00001*; do mv "$i" "${i/F00001/F0001}"; done
or, portably,
for i in F00001*; do mv "$i" "F0001${i#F00001}"; done
This replaces the F00001 prefix in the filenames with F0001.
credits to mahesh here: http://www.debian-administration.org/articles/150
The sed command
s/\(.\).\(.*\)/mv & \1\2/
means to replace:
\(.\).\(.*\)
with:
mv & \1\2
just like a regular sed command. However, the parentheses, & and \n markers change it a little.
The search string matches (and remembers as pattern 1) the single character at the start, followed by a single character, follwed by the rest of the string (remembered as pattern 2).
In the replacement string, you can refer to these matched patterns to use them as part of the replacement. You can also refer to the whole matched portion as &.
So what that sed command is doing is creating a mv command based on the original file (for the source) and character 1 and 3 onwards, effectively removing character 2 (for the destination). It will give you a series of lines along the following format:
mv F00001-0708-RG-biasliuyda F0001-0708-RG-biasliuyda
mv abcdef acdef
and so on.
Using perl rename (a must have in the toolbox):
rename -n 's/0000/000/' F0000*
Remove -n switch when the output looks good to rename for real.
There are other tools with the same name which may or may not be able to do this, so be careful.
The rename command that is part of the util-linux package, won't.
If you run the following command (GNU)
$ rename
and you see perlexpr, 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 apt install rename
$ sudo update-alternatives --set rename /usr/bin/file-rename
For archlinux:
pacman -S perl-rename
For RedHat-family distros:
yum install prename
The 'prename' package is in the EPEL repository.
For Gentoo:
emerge dev-perl/rename
For *BSD:
pkg install gprename
or p5-File-Rename
For Mac users:
brew install rename
If you don't have this command with another distro, search your package manager to install it or do it manually:
cpan -i File::Rename
Old standalone version can be found here
man rename
This tool was originally written by Larry Wall, the Perl's dad.
The backslash-paren stuff means, "while matching the pattern, hold on to the stuff that matches in here." Later, on the replacement text side, you can get those remembered fragments back with "\1" (first parenthesized block), "\2" (second block), and so on.
If all you're really doing is removing the second character, regardless of what it is, you can do this:
s/.//2
but your command is building a mv command and piping it to the shell for execution.
This is no more readable than your version:
find -type f | sed -n 'h;s/.//4;x;s/^/mv /;G;s/\n/ /g;p' | sh
The fourth character is removed because find is prepending each filename with "./".
Here's what I would do:
for file in *.[Jj][Pp][Gg] ;do
echo mv -vi \"$file\" `jhead $file|
grep Date|
cut -b 16-|
sed -e 's/:/-/g' -e 's/ /_/g' -e 's/$/.jpg/g'` ;
done
Then if that looks ok, add | sh to the end. So:
for file in *.[Jj][Pp][Gg] ;do
echo mv -vi \"$file\" `jhead $file|
grep Date|
cut -b 16-|
sed -e 's/:/-/g' -e 's/ /_/g' -e 's/$/.jpg/g'` ;
done | sh
for i in *; do mv $i $(echo $i|sed 's/AAA/BBB/'); done
The parentheses capture particular strings for use by the backslashed numbers.
ls F00001-0708-*|sed 's|^F0000\(.*\)|mv & F000\1|' | bash
Some examples that work for me:
$ tree -L 1 -F .
.
├── A.Show.2020.1400MB.txt
└── Some Show S01E01 the Loreming.txt
0 directories, 2 files
## remove "1400MB" (I: ignore case) ...
$ for f in *; do mv 2>/dev/null -v "$f" "`echo $f | sed -r 's/.[0-9]{1,}mb//I'`"; done;
renamed 'A.Show.2020.1400MB.txt' -> 'A.Show.2020.txt'
## change "S01E01 the" to "S01E01 The"
## \U& : change (here: regex-selected) text to uppercase;
## note also: no need here for `\1` in that regex expression
$ for f in *; do mv 2>/dev/null "$f" "`echo $f | sed -r "s/([0-9] [a-z])/\U&/"`"; done
$ tree -L 1 -F .
.
├── A.Show.2020.txt
└── Some Show S01E01 The Loreming.txt
0 directories, 2 files
$
2>/dev/null suppresses extraneous output (warnings ...)
reference [this thread]: https://stackoverflow.com/a/2372808/1904943
change case: https://www.networkworld.com/article/3529409/converting-between-uppercase-and-lowercase-on-the-linux-command-line.html