I want to change file names in a folder in a way like this:
previous form new form
one-1 to VAS-M0001-001
one-2 to VAS-M0001-002
one-3 to VAS-M0001-003
one-4 to VAS-M0001-004
Can anyone please suggest me a good way to do that?
I would just use a simple loop:
for f in one-*; do mv one-$f VAS-M001-000$f; done
Of course, you can use printf to format the number better (if you have more than 9 files)
rename has such a functionality
[username#hostname aa]$ touch one-1 one-2 one-3 one-4
[username#hostname aa]$ ls
one-1 one-2 one-3 one-4
[username#hostname aa]$ rename one- VAS-M0001-000 one*
[username#hostname aa]$ ls
VAS-M0001-0001 VAS-M0001-0002 VAS-M0001-0003 VAS-M0001-0004
Related
We have a tool for cutting adaptors https://github.com/vsbuffalo/scythe/blob/master/README.md and we wanted it to be used on all the files in the raw folder and make an output of each file separately as OUT+File Name.
Something is wrong with this script I wrote, because it doesn't take each file separately, and the whole thing doesn't work properly. It's gonna generateing empty file named OUT+files
Expected operation will looks:
take file1, use scythe on it, write output as OUTfile1
take file2 etc.
#!/bin/bash
FILES=/home/dave/raw/*
for f in $FILES
do
echo "Processing the $f file..."
/home/deve/scythe/scythe -a /home/dev/scythe/illumina_adapters.fa -o "OUT"+$f $f
done
Additionally, I noticed (testing for a single file) that the script uses only one core out of 130 available. Is there any way to improve it?
There is no string concatenation operator in shell. Use juxtaposition instead; it's "OUT$f", not "OUT"+$f.
How can I pass each one of my repository files and to do something with them?
For instance, I want to make a script:
#!/bin/bash
cd /myself
#for-loop that will select one by one all the files in /myself
#for each X file I will do this:
tar -cvfz X.tar.gz /myself2
So a for loop in bash is similar to python's model (or maybe the other way around?).
The model goes "for instance in list":
for some_instance in "${MY_ARRAY[#]}"; do
echo "doing something with $some_instance"
done
To get a list of files in a directory, the quick and dirty way is to parse the output of ls and slurp it into an array, a-la array=($(ls))
To quick explain what's going on here to the best of my knowledge, assigning a variable to a space-delimited string surrounded with parens splits the string and turns it into a list.
Downside of parsing ls is that it doesn't take into account files with spaces in their names. For that, I'll leave you with a link to turning a directory's contents into an array, the same place I lovingly :) ripped off the original array=($(ls -d */)) command.
you can use while loop, as it will take care of whole lines that include spaces as well:
#!/bin/bash
cd /myself
ls|while read f
do
tar -cvfz "$f.tar.gz" "$f"
done
you can try this way also.
for i in $(ls /myself/*)
do
tar -cvfz $f.tar.gz /myfile2
done
I want to add the ".sbd" after all files ending on ".utf8" in a directory
I do not want to replace the extensions, but really want to add them so the filenames will look like "filename.utf8.sbd"
I think I should adapt the following code, but don't manage to find out exactly how
for f in *.utf8 ; do mv "$f" "$f.sbd" ; done
Can anyone help me? I am very new to the command line
Thanks a bunch!
Your code should work if no file has spaces (or other "special" character) in the name and if the directory is not pathologically big.
In those cases, you can use something like this:
ls|grep '*.utf8$'|while read i; do mv "$i" "$i.sbd"; done
I need to rename hundreds of files in Linux to change the unique identifier of each from the command line. For sake of examples, I have a file containing:
old_name1 new_name1
old_name2 new_name2
and need to change the names from new to old IDs. The file names contain the IDs, but have extra characters as well. My plan is therefore to end up with:
abcd_old_name1_1234.txt ==> abcd_new_name1_1234.txt
abcd_old_name2_1234.txt ==> abcd_new_name2_1234.txt
Use of rename is obviously fairly helpful here, but I am struggling to work out how to iterate through the file of the desired name changes and pass this as input into rename?
Edit: To clarify, I am looking to make hundreds of different rename commands, the different changes that need to be made are listed in a text file.
Apologies if this is already answered, I've has a good hunt, but can't find a similar case.
rename 's/^(abcd_)old_name(\d+_1234\.txt)$/$1new_name$2/' *.txt
Should work, depending on whether you have that package installed. Also have a look at qmv (rename-utils)
If you want more options, use e.g.
shopt -s globstart
rename 's/^(abcd_)old_name(\d+_1234\.txt)$/$1new_name$2/' folder/**/*.txt
(finds all txt files in subdirectories of folder), or
find folder -type f -iname '*.txt' -exec rename 's/^(abcd_)old_name(\d+_1234\.txt)$/$1new_name$2/' {} \+
To do then same using GNU find
while read -r old_name new_name; do
rename "s/$old_name/$new_name/" *$old_name*.txt
done < file_with_names
In this way, you read the IDs from file_with_names and rename the files replacing $old_name with $new_name leaving the rest of the filename untouched.
I was about to write a php function to do this for myself, but I came upon a faster method:
ls and copy & paste the directory contents into excel from the terminal window. Perhaps you may need to use on online line break removal or addition tool. Assume that your file names are in column A In excel, use the following formula in another column:
="mv "&A1&" prefix"&A1&"suffix"
or
="mv "&A1&" "&substitute(A1,"jpeg","jpg")&"suffix"
or
="mv olddirectory/"&A1&" newdirectory/"&A1
back in Linux, create a new file with
nano rename.txt and paste in the values from excel. They should look something like this:
mv oldname1.jpg newname1.jpg
mv oldname1.jpg newname2.jpg
then close out of nano and run the following command:
bash rename.txt. Bash just runs every line in the file as if you had typed it.
and you are done! This method gives verbose output on errors, which is handy.
i have a set of files named img1.png , img2.png ,...img10.png,.. and so on. what i want to achieve is renaming these files so that the starting index is increased by 30 such that the files become img31.png, img32.png,.....img40.png,....and so on. Is this possible using the "rename" command? or is a script required? in either case how do i do this?
related - for this to work do i have to first rename the files to img001.png, img002.png, ...img010.png , and so on? how is this to be done, if required?
add 30 to the numbers in each filename
rename 's/(\d+)/$1+30/e' *png
rename to be 3 digits long
rename 's/(\d+)/sprintf("%03d",$1)/e' *png
See perldoc perlre http://perldoc.perl.org/perlre.html for details of how this works, rename is a perl program
LOCATION=/my/image/directory #change this to your location
for file in $(ls -1 ${LOCATION})
do
ind=$(echo ${file}|cut -c 4-|cut -d"." -f1)
(( newind=${ind}+30 ))
mv ${LOCATION}/${file} ${LOCATION}/img${newind}.png
done
I am sure there is much more elegant way of doing this on one line using likes of awk/sed/perl etc, but this shows you the logic behind it.
Hope it helps