I have several fastq.gz files in a directory. I want to delete parts of each file name.
Here are the file names:
RES_1448_001_S289_L001_R1_001.fastq.gz
RES_1448_001_S289_L001_R2_001.fastq.gz
RES_1448_012_S300_L001_R1_001.fastq.gz
RES_1448_012_S300_L001_R2_001.fastq.gz
I want to remove S and 3 digits after it. I expect this after removing
RES_1448_001_R1_001.fastq.gz
RES_1448_001_R2_001.fastq.gz
RES_1448_012_R1_001.fastq.gz
RES_1448_012_R2_001.fastq.gz
I asked a similar question before, but was advised to ask a new one to cover the precise requirements I have now.
Old question: Delete part of name of multiple files in Linux
Use rename.
rename 's/S\d{3}_//' *.fastq.gz
Using this bash, regEx would do the trick for you.
#!/bin/bash
for file in *.fastq.gz
do
if [[ $file =~ ^(.*)S([[:digit:]]{3})_L([[:digit:]]{3})_(.*)$ ]]
then
start="${BASH_REMATCH[1]}"
end="${BASH_REMATCH[4]}"
mv -- "$file" "${start}${end}"
fi
done
Related
I have video files with this structure : GX**#### where #### is the number of the video.
But sometimes videos are splitted in 2 or 3 files, for instance : GX01#### and GX02####
My problem is that to organise my folders I prefer rename them like this : GX####-1 and GX####-2.
So i ask you the question if I can create a script/command to rename automatically my files to do this ? I can use .bat windows files or .sh linux files. My main problem is that i don't know a command to rename files simply (i saw many solutions which rewrite the entire file). May be if you know just this I will can do my script.
Thanks you in advance.
You can loop through the files and use PE parameter expansion to slice and jumble the strings and mv to rename the files.
Here is an example, first let us create an empty files using touch, but first we need to create a new directory (folder as you call it) and go into that newly created directory, using mkdir and cd.
mkdir newdirectory && cd newdirectory
Now create the empty files using touch.
touch GX01#### GX02#### GX03#### GX04####
Now check the empty files using ls
ls *
The output should be like
GX01#### GX02#### GX03#### GX04####
Now that we have created empty files, we can now do the renaming part.
for file in GX*; do
file1="${file#*??}"
file2=${file1#*??}
file3=${file1%*$file2}
echo mv -v "$file" "${file%*$file1}${file2}"-"$file3"
done
The output should be on stdout (which is your screen) because of the echo.
mv -v GX01#### GX####-01
mv -v GX02#### GX####-02
mv -v GX03#### GX####-03
mv -v GX04#### GX####-04
If you're satisfied with what you see then remove the echo, so mv can actually rename the files. To show how the slicing is done here is an example.
file=GX01####
file1="${file#*??}"
file2=${file1#*??}
file3="${file1%*$file2}"
printf '%s\n' "$file1" "$file2" "$file3"
The output should be something like.
01####
####
01
The ? means a single string from the shell.
A word of caution and advice, make a backup of the files you want to edit just in case the shell made a mistake while you're renaming the files. :-)
Also you should probably use shell globing like nullglob see
http://mywiki.wooledge.org/glob#nullglob
See man bash and look for Parameter Expansion.
PAGER='less +/^[[:space:]]*parameter\ expansion' man bash
Some online resources, with detailed explanation and examples.
http://mywiki.wooledge.org/BashFAQ/073
https://wiki.bash-hackers.org/syntax/pe
You could echo the original and new file names:
for f in GX*; do
echo "$f" $(sed 's/^GX\(..\)\(.*\)/GX\2-\1/' <<< "$f")
done
which should output:
GX01#### GX####-01
GX02#### GX####-02
then use mv -n instead of echo to rename the files.
I have a bunch of files (more than 1000) on this like the followings
$ ls
org.allenai.ari.solvers.termselector.BaselineLearnersurfaceForm-dev.lc
org.allenai.ari.solvers.termselector.BaselineLearnersurfaceForm-dev.lex
org.allenai.ari.solvers.termselector.BaselineLearnersurfaceForm-train.lc
org.allenai.ari.solvers.termselector.BaselineLearnersurfaceForm-train.lex
org.allenai.ari.solvers.termselector.BaselineLearnersurfaceForm.lc
org.allenai.ari.solvers.termselector.BaselineLearnersurfaceForm.lex
org.allenai.ari.solvers.termselector.ExpandedLearner.lc
org.allenai.ari.solvers.termselector.ExpandedLearner.lex
org.allenai.ari.solvers.termselector.ExpandedLearnerSVM.lc
org.allenai.ari.solvers.termselector.ExpandedLearnerSVM.lex
....
I have to rename these files files by adding a learners right before the capitalized name. For example
org.allenai.ari.solvers.termselector.BaselineLearnersurfaceForm.lex
would change to
org.allenai.ari.solvers.termselector.learners.BaselineLearnersurfaceForm.lex
and this one
org.allenai.ari.solvers.termselector.ExpandedLearner.lc
would change to
org.allenai.ari.solvers.termselector.learners.ExpandedLearner.lc
Any ideas how to do this automatically?
for f in org.*; do
echo mv "$f" "$( sed 's/\.\([A-Z]\)/.learner.\1/' <<< "$f" )"
done
This short loop outputs an mv command that renames the files in the manner that you wanted. Run it as-is first, and when you are certain it's doing what you want, remove the echo and run again.
The sed bit in the middle takes a filename ($f, via a here-string, so this requires bash) and replaces the first occurrence of a capital letter after a dot with .learner. followed by that same capital letter.
There is a tool called perl-rename, sometimes rename. Not to be confused with rename from util-linux.
It's very good for tasks like this as it takes a perl expression and renames accordingly:
perl-rename 's/(?=\.[A-Z])/.learners/' *
You can play with the regex online
Alternative you can a for loop and $BASH_REMATCH:
for file in *; do
[ -e "$file" ] || continue
[[ "$file" =~ ^([^A-Z]*)(.*)$ ]]
mv -- "$file" "${BASH_REMATCH[1]}learners.${BASH_REMATCH[2]}"
done
A very simple approach (useful if you only need to do this one time) is to ls >dummy them into a text file dummy, and then use find/replace in a text editor to make lines of the form mv xxx.yyy xxx.learners.yyy. Then you can simple execute the resulting file with ./dummy.
The exact find/replace commands depend on the text editor you use, but something like
replace org. with mv org.. That gets you the mv in the beginning.
replace mv org.allenai.ari.solvers.termselector.$1 with mv org.allenai.ari.solvers.termselector.$1 org.allenai.ari.solvers.termselector.learner.$1 to duplicate the filename and insert the learner.
There is also syntax with a for, which can do it probably in one line, (long) but I cannot explain it - try help for if you want to learn about it.
I have over a thousand files of similar names in a directory and wish to do a rename. The files are of this format
GW_LGMS01-50160306185154-01375272.CDR
GW_LGMS01-50160306237154-01375272.CDR.00001
GW_LGMS02-50160306133554-02308872.CDR
GW_LGMS02-50160306137554-02308872.CDR.00014
GW_LGMS03-50160306221836-02217475.CDR.00001
GW_LGMS03-50160306235132-02217475.CDR
I want to do a rename on all of them at once to append a 0- before 50160306 on all of them. That is,
GW_LGMS01-0-50160306185154-01375272.CDR
GW_LGMS01-0-50160306237154-01375272.CDR.00001
GW_LGMS02-0-50160306133554-02308872.CDR
GW_LGMS02-0-50160306137554-02308872.CDR.00014
GW_LGMS03-0-50160306221836-02217475.CDR.00001
GW_LGMS03-0-50160306235132-02217475.CDR
50160306 is what all the files have in common.
Assuming that -50160306 is unique in the file names, and that you are using a shell that understands ${parameter/pattern/string} (Bash, KornShell, etc.):
for f in *.CDR*; do
echo mv "$f" "${f/-50160306/-0-50160306}"
done
Do this with the echo in place to see what would happen, then remove the echo when you are sure it does the right thing.
If you are afraid to mess up, just put the files with the new names in a new folder:
mkdir renamed
for f in *.CDR*; do
cp "$f" renamed/"${f/-50160306/-0-50160306}"
done
If you don't use bash:
#!/bin/sh
for i in * ; do
mv "$i" "$(printf '%s' "$i" | sed 's/\(50160306.*\)/0-\1/')"
done
There are two rename tools floating around: one is part of the util-linux package, the other is Perl based (see this answer for details). To find out which one you have, check at the end of the man page (man rename).
With the util-linux version, you can rename your files as follows:
rename 50160306 0-50160306 *
and for the Perl based version, it would be (untested!)
rename 's/50160306/0-$&/' *
Be aware that there are no safeguards with these commands – test them on a small sample before you use them.
I'm trying to learn how to batch edit files and extract information from them. I've begun with trying to create some trial files and editing their names. I tried to search but couldn't find the problem I'm in anywhere.
If it's already answered, I'd be happy to be directed to that link.
So, I wrote the following code:
#!/bin/bash
mkdir -p ./trialscript
echo $1
i=1
while [ $i -le $1 ]
do
touch ./trialscript/testfile$i.dat
i=$(($i+1))
done
for f in ./trialscript/*.dat
do
echo $f
mv "$f" "$fhello.dat"
done
This doesn't seem to work, and I think it's because the echo output is like:
4
./trialscript/testfile1.dat
./trialscript/testfile2.dat
./trialscript/testfile3.dat
./trialscript/testfile4.dat
I just need the filename in the 'f' and not the complete path and then just rename it.
Can someone suggest what is wrong in my code, and what's correct way to do what I'm doing.
If you want to move the file, you have to use the path, too, otherwise mv wouldn't be able to find it.
The target specification for the mv command is more problematic, though. You're using
"$fhello.dat"
which, in fact, means "content of the $fhello variable plus the string .dat". How should the poor shell know where the seam is? Use
"${f}hello.dat"
to disambiguate.
Also, to extract parts of strings, see Parameter expansion in man bash. You can use ${f%/*} to only get the path, or ${f##*/} to only get the filename.
I am very new with linux usage maybe this is my first time so i hope some detailed help please.
I have more than 500 files in multiple directories on my server (Linux) I want to change their extensions to .xml using bash script
I used a lot of codes but none of them work some codes i used :
for file in *.txt
do
mv ${file} ${file/.txt}/.xml
done
or
for file in *.*
do
mv ${file} ${file/.*}/.xml
done
i do not know even if the second one is valid code or not i tried to change the txt extension beacuse the prompt said no such file '.txt'
I hope some good help for that thank you
Explanation
For recursivity you need Bash >=4 and to enable ** (i.e. globstar) ;
First, I use parameter expansion to remove the string .txt, which must be anchored at the end of the filename (%) :
the # anchors the pattern (plain word or glob) to the beginning,
and the % anchors it to the end.
Then I append the new extension .xml
Be extra cautious with filename, you should always quote parameters expansion.
Code
This should do it in Bash (note that I only echothe old/new filename, to actually rename the files, use mv instead of echo) :
shopt -s globstar # enable ** globstar/recursivity
for i in **/*.txt; do
[[ -d "$i" ]] && continue; # skip directories
echo "$i" "${i/%.txt}.xml";
done
If its a matter of a one or two sub-directories, you can use the rename command:
rename .txt .xml *.txt
This will rename all the .txt to .xml files in the directory from which the command is executed.
If all the files are in same directory, it can be done using a single command. For example you want to convert all jpg files to png, go to the related directory location and then use command
rename .jpg .png *
I wanted to rename "file.txt" to "file.jpg.txt", used rename easy peezy:
rename 's/.txt$/.jpg.txt/' *.txt
man rename will tell you everything you need to know.
Got to love Linux, there's a tool for everything :-)
passing command line argument for dir path
#!/bin/sh
cd $1
names_1=`ls`
for file in ${names_1}
do
mv ${file} ${file}.jpg
done