I'm trying to iterate through all the files in a directory and rename them from the prefix ABC to XYZ using the command below
while read file; do mv \"$file\" \"$(echo $file | sed -e s/ABC/XYZ/g)\" ; done < <(ls -1)
When I throw an echo in front of the mv, everything looks like it should work fine and copy/pasting the outputted command works fine but it won't execute correctly within the context of the loop giving me a usage error as if the command is malformed like below.
usage: mv [-f | -i | -n] [-v] source target
mv [-f | -i | -n] [-v] source ... directory
Even though the outputted command from the check with echo gives
mv "ABC Test1" "XYZ Test1"
which should be a valid command and works if I copy paste.
Any idea what is going on?
Relace:
while read file; do mv \"$file\" \"$(echo $file | sed -e s/ABC/XYZ/g)\" ; done < <(ls -1)
With:
for file in *
do
mv "$file" "${file//ABC/XYZ}"
done
Notes:
This is very important: Never parse ls. ls is only designed to produce human-friendly output.
To iterate over all files in a directory, use for file in *; do ...; done. This will work reliably for all manor of file names including file names with newlines, blanks, or other difficult characters.
\" produces a literal character, not a syntactic character. Since we want the syntactic meaning of " here, we leave it unescaped.
There are times when one needs sed but this isn't one of them.
The shell is capable of doing simple substitutions without all the issues associated with command substitution. Thus, $(echo $file | sed -e s/ABC/XYZ/g) can be replaced with ${file//ABC/XYZ}.
The form ${var//old/new} is called pattern substitution and is documented in man bash.
Very stupid mistake. There was no need to escape the quotes in the mv command. Taking those out makes it work as expected. Escaping the quotes shows the correct output with echo but does not give intended behavior.
while read file; do mv "$file" "$(echo $file | sed -e s/ABC/XYZ/g)" ; done < <(ls -1)
Related
I am new with Bash, and trying to rename files in my folder keeping the first 9 characters intact and get rid of anything that comes after.
abc123456olda.jpg > abc123456.jpg
I wrote this;
for file in *
do
echo mv "$file" `echo "$file" | sed -e 's/(.{9}).*(\.jpg)$/$1$2/' *.jpg
done
Did not get it to work. Can someone guide what am I doing wrong?
You're not far off, try this:
for file in *.jpg; do
echo mv "$file" "$(echo "$file" | sed -E -e 's/(.{9}).*(\.jpg)$/\1\2/')"
done
There are some corrections. A important one is that $1$2 should be \1\2, and you need the -E flag to sed so that it understands the grouping with parenthesis.
Once you see the command is alright, remove the echo from the second line so mv actually gets executed.
Use bash's built-in parameter expansion operator rather than sed.
Also, you should put *.jpg in the for statement, not the sed argument; what you're doing is processing the contents of the files, not the filenames.
for file in *.jpg
do
mv "$file" "${file:0:9}.jpg"
done
${file:0:9} means the substring of $file starting from index 0 and having 9 characters.
I have a list of filenames like this in bash
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R1.fq.gz
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R1.fq.gz
UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R2.fq.gz
And I want them to look like this
UTSHoS10_R1.fq.gz
UTSHoS10_R2.fq.gz
UTSHoS11_R1.fq.gz
UTSHoS11_R2.fq.gz
UTSHoS12_R1.fq.gz
UTSHoS12_R2.fq.gz
I do not have the perl rename command and sed 's/_Other*160418./_/' *.gz
is not doing anything. I've tried other rename scripts on here but either nothing occurs or my shell starts printing huge amounts of code to the console and freezes.
This post (Removing Middle of Filename) is similar however the answers given do not explain what specific parts of the command are doing so I could not apply it to my problem.
Parameter expansions in bash can perform string substitutions based on glob-like patterns, which allows for a more efficient solution than calling an extra external utility such as sed in each loop iteration:
for f in *.gz; do echo mv "$f" "${f/_Other_*-TTAGGA_R_160418./_}"; done
Remove the echo before mv to perform actual renaming.
You can do something like this in the directory which contains the files to be renamed:
for file_name in *.gz
do
new_file_name=$(sed 's/_[^.]*\./_/g' <<< "$file_name");
mv "$file_name" "$new_file_name";
done
The pattern (_[^.]*\.) starts matching from the FIRST _ till the FIRST . (both inclusive). [^.]* means 0 or more non-dot (or non-period) characters.
Example:
AMD$ ls
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R1.fq.gz UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R1.fq.gz
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R2.fq.gz UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
AMD$ for file_name in *.gz
> do new_file_name=$(sed 's/_[^.]*\./_/g' <<< "$file_name")
> mv "$file_name" "$new_file_name"
> done
AMD$ ls
UTSHoS10_R1.fq.gz UTSHoS10_R2.fq.gz UTSHoS11_R2.fq.gz UTSHoS12_R1.fq.gz UTSHoS12_R2.fq.gz
Pure Bash, using substring operation and assuming that all file names have the same length:
for file in UTS*.gz; do
echo mv -i "$file" "${file:0:9}${file:38:8}"
done
Outputs:
mv -i UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R1.fq.gz UTSHoS10_R1.fq.gz
mv -i UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R2.fq.gz UTSHoS10_R2.fq.gz
mv -i UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz UTSHoS11_R2.fq.gz
mv -i UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz UTSHoS11_R2.fq.gz
mv -i UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R1.fq.gz UTSHoS12_R1.fq.gz
mv -i UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R2.fq.gz UTSHoS12_R2.fq.gz
Once verified, remove echo from the line inside the loop and run again.
Going with your sed command, this can work as a bash one-liner:
for name in UTSH*fq.gz; do newname=$(echo $name | sed 's/_Other.*160418\./_/'); echo mv $name $newname; done
Notes:
I've adjusted your sed command: it had an * without a preceeding . (sed takes a regular expression, not a globbing pattern). Similarly, the dot needs escaping.
To see if it works, without actually renaming the files, I've left the echo command in. Easy to remove just that to make it functional.
It doesn't have to be a one-liner, obviously. But sometimes, that makes editing and browsing your command-line history easier.
The script works as far as renaming the files but it moves the renamed files out of their respective folders.
I would like it to not move them but only rename them and I have failed after a few days of trying. I know this code is a mess and there is unneeded code in it but it nearly works.
Also the renamed file isn’t getting an extension of .txt but that isn't really an issue for me. I just want to see the "Dynamic Range Value" that is taken from inside the file as the file name so I don’t have to open every file (a couple thousand albums worth) to see what the DR is. Here is the code:
#!/bin/bash
cd /media/Storage/MusicWorks/Processing
find . -name 'dr14.txt' | while IFS=$'\n' read -r i
do mv -n "$i" `egrep -m1 -e 'Official DR value:' "$i" | sed -e 's/Official DR value://'`;
echo "Done"
done
I run this script from the terminal with a bash alias.
I have reservations about the egrep | sed part of your script, but if they work for you, so be it. You need to preserve the pathname of the file, for example like this:
find . -name 'dr14.txt' |
while IFS=$'\n' read -r i
do
newname="${i%/*}"/$(egrep -m1 -e 'Official DR value:' "$i" | sed -e 's/Official DR value://');
mv -n "$i" "$newname"
echo "Done $i ($newname)"
done
The ${i%/*} notation removes anything from the last slash to the end of the name in $i. Since all the names from find will start with ./, this is secure enough; it would not work well on absolute names such as / and /unix (the output would be the empty string, but /usr/bin/sh would be fine).
Under a little prompting by tripleee in a comment, it is possible to simplify the egrep | sed part of the code to:
newname="${i%/*}"/$(sed -n -e '/Official DR value:/{s///p;q;}' "$i");
The second semicolon is needed with BSD sed but not with GNU sed.
I have the following files in the following format:
$ ls CombinedReports_LLL-*'('*.csv
CombinedReports_LLL-20140211144020(Untitled_1).csv
CombinedReports_LLL-20140211144020(Untitled_11).csv
CombinedReports_LLL-20140211144020(Untitled_110).csv
CombinedReports_LLL-20140211144020(Untitled_111).csv
CombinedReports_LLL-20140211144020(Untitled_12).csv
CombinedReports_LLL-20140211144020(Untitled_13).csv
CombinedReports_LLL-20140211144020(Untitled_14).csv
CombinedReports_LLL-20140211144020(Untitled_15).csv
CombinedReports_LLL-20140211144020(Untitled_16).csv
CombinedReports_LLL-20140211144020(Untitled_17).csv
CombinedReports_LLL-20140211144020(Untitled_18).csv
CombinedReports_LLL-20140211144020(Untitled_19).csv
I would like this part removed:
20140211144020 (this is the timestamp the reports were run so this will vary)
and end up with something like:
CombinedReports_LLL-(Untitled_1).csv
CombinedReports_LLL-(Untitled_11).csv
CombinedReports_LLL-(Untitled_110).csv
CombinedReports_LLL-(Untitled_111).csv
CombinedReports_LLL-(Untitled_12).csv
CombinedReports_LLL-(Untitled_13).csv
CombinedReports_LLL-(Untitled_14).csv
CombinedReports_LLL-(Untitled_15).csv
CombinedReports_LLL-(Untitled_16).csv
CombinedReports_LLL-(Untitled_17).csv
CombinedReports_LLL-(Untitled_18).csv
CombinedReports_LLL-(Untitled_19).csv
I was thinking simply along the lines of the mv command, maybe something like this:
$ ls CombinedReports_LLL-*'('*.csv
but maybe a sed command or other would be better
rename is part of the perl package. It renames files according to perl-style regular expressions. To remove the dates from your file names:
rename 's/[0-9]{14}//' CombinedReports_LLL-*.csv
If rename is not available, sed+shell can be used:
for fname in Combined*.csv ; do mv "$fname" "$(echo "$fname" | sed -r 's/[0-9]{14}//')" ; done
The above loops over each of your files. For each file, it performs a mv command: mv "$fname" "$(echo "$fname" | sed -r 's/[0-9]{14}//')" where, in this case, sed is able to use the same regular expression as the rename command above. s/[0-9]{14}// tells sed to look for 14 digits in a row and replace them with an empty string.
Without using an other tools like rename or sed and sticking strictly to bash alone:
for f in CombinedReports_LLL-*.csv
do
newName=${f/LLL-*\(/LLL-(}
mv -i "$f" "$newName"
done
for f in CombinedReports_LLL-* ; do
b=${f:0:20}${f:34:500}
mv "$f" "$b"
done
You can try line by line on shell:
f="CombinedReports_LLL-20140211144020(Untitled_11).csv"
b=${f:0:20}${f:34:500}
echo $b
You can use the rename utility for this. It uses syntax much like sed to change filenames. The following example (from the rename man-page) shows how to remove the trailing '.bak' extension from a list of backup files in the local directory:
rename 's/\.bak$//' *.bak
I'm using the advice given in the top response and have put the following line into a shell script:
ls *.nii | xargs rename 's/[f_]{2}//' f_0*.nii
In terminal, this line works perfectly, but in my script it will not execute and reads * as a literal part of the file name.
I am trying to modify a bash script to remove a glob of malicious code from a large number of files.
The community will benefit from this, so here it is:
#!/bin/bash
grep -r -l 'var createDocumentFragm' /home/user/Desktop/infected_site/* > /home/user/Desktop/filelist.txt
for i in $(cat /home/user/Desktop/filelist.txt)
do
cp -f $i $i.bak
done
for i in $(cat /home/user/Desktop/filelist.txt)
do
$i | sed 's/createDocumentFragm.*//g' > $i.awk
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
This is where the script bombs out with this message:
+ for i in '$(cat /home/user/Desktop/filelist.txt)'
+ sed 's/createDocumentFragm.*//g'
+ /home/user/Desktop/infected_site/index.htm
I get 2 errors and the script stops.
/home/user/Desktop/infected_site/index.htm: line 1: syntax error near unexpected token `<'
/home/user/Desktop/infected_site/index.htm: line 1: `<html><head><script>(function (){ '
I have the first 2 parts done.
The files containing createDocumentfragm have been enumerated in a text file correctly.
The files in the textfile.txt have been duplicated, in their original location with a .bak added to them IE: infected_site/some_directory/infected_file.htm and infected_file.htm.bak
effectively making sure we have a backup.
All I need to do now is write an AWK command that will use the list of files in filelist.txt, use the entire glob of malicious text as a pattern, and remove it from the files. Using just the uppercase script as the starting point, and the lower case script is too generic and could delete legitimate text
I suspect this may help me, but I don't know how to use it correctly.
http://backreference.org/2010/03/13/safely-escape-variables-in-awk/
Once I have this part figured out, and after you have verified that the files weren't mangled you can do this to clean out the bak files:
for i in $(cat /home/user/Desktop/filelist.txt)
do
rm -f $i.bak
done
Several things:
You have:
$i | sed 's/var createDocumentFragm.*//g' > $i.awk
You should probably meant this (using your use of cat which we'll talk about in a moment):
cat $i | sed 's/var createDocumentFragm.*//g' > $i.awk
You're treating each file in your file list as if it was a command and not a file.
Now, about your use of cat. If you're using cat for almost anything but concatenating multiple files together, you probably are doing something not quite right. For example, you could have done this:
sed 's/var createDocumentFragm.*//g' "$i" > $i.awk
I'm also a bit confused about the awk statement. Exactly what file are you using awk on? Your awk statement is using STDIN and STDOUT, so it's reading file names from the for loop and then printing the output on the screen. Is the sed statement suppose to feed into the awk statement?
Note that I don't have to print out my file to STDOUT, then pipe that into sed. The sed command can take the file name directly.
You also want to avoid for loops over a list of files. That is very inefficient, and can cause problems with the command line getting overloaded. Not a big issue today, but can affect you when you least suspect it. What happens is that your $(cat /home/user/Desktop/filelist.txt) must execute first before the for loop can even start.
A little rewriting of your program:
cd ~/Desktop
grep -r -l 'var createDocumentFragm' infected_site/* > filelist.txt
while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" > "$i.awk"
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
done < filelist.txt
We can use one loop, and we made it a while loop. I could even feed the grep into that while loop:
grep -r -l 'var createDocumentFragm' infected_site/* | while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" > "$i.awk"
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
done < filelist.txt
and then I don't even have to create a temporary file.
Let me know what's going on with the awk. I suspect you wanted something like this:
grep -r -l 'var createDocumentFragm' infected_site/* | while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" \
| awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p' > "$i.awk"
done < filelist.txt
Also note I put quotes around file names. This helps prevent problems if file name has a space in it.