I'm using for loop, with arguments i. Each argument contains ".net" at the end and in directory they are in one line, divided by some space. Now I need to get rid of these ".net" using substitution of sed, but it's not working. I went through different options, the most recent one is
sed 's/\.(net)//g' $i;
which is obviously not correct, but I just can't find anything online about this.
To make it clear, lets say I have a directory with 5 files with names
file1.net
file2.net
file3.net
file4.net
file5.net
I would like my output to be
file1
file2
file3
file
file5
...Could somebody give me some advice?
You can use
for f in *.net; do mv "$f" "${f%.*}"; done
Details:
for f in *.net; - iterates over files with net extension
mv "$f" "${f%.*}" - renames the files with the file without net extension (${f%.*} removes all text - as few as possible - from the end of f till the first ., see Parameter expansion).
This is a work for perl's rename :
rename -n 's/\.net//' *.net
The -n is for test purpose. Remove it if the output looks good for you
This way:
sed -i.backup 's/\.net$//g' "$1";
It will create a backup for safeness
Related
I have a directory with multiple fasta file named as followed:
BC-1_bin_1_genes.faa
BC-1_bin_2_genes.faa
BC-1_bin_3_genes.faa
BC-1_bin_4_genes.faa
etc. (about 200 individual files)
The fasta header look like this:
>BC-1_k127_3926653_6 # 4457 # 5341 # -1 # ID=2_6;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.697
I now want to add the filename to the header since I want to annotate the sequences for each file.I tried the following:
for file in *.faa;
do
sed -i "s/>.*/${file%%.*}/" "$file" ;
done
It worked partially but it removed the ">" from the header which is essential for the fasta file. I tried to modify the "${file%%.*}" part to keep the carrot but it always called me out on bad substitutions.
I also tried this:
awk '/>/{sub(">","&"FILENAME"_");sub(/\.faa/,x)}1' *.faa
This worked in theory but only printed everything on my terminal rather than changing it in the respective files.
Could someone assist with this?
It's not clear whether you want to replace the earlier header, or add to it. Both scenarios are easy to do. Don't replace text you don't want to replace.
for file in ./*.faa;
do
sed -i "s/^>.*/>${file%%.*}/" "$file"
done
will replace the header, but include a leading > in the replacement, effectively preserving it; and
for file in ./*.faa;
do
sed -i "s/^>.*/&${file%%.*}/" "$file"
done
will append the file name at the end of the header (& in the replacement string evaluates to the string we are replacing, again effectively preserving it).
For another variation, try
for file in *.faa;
do
sed -i "/^>/s/\$/ ${file%%.*}/" "$file"
done
which says on lines which match the regex ^>, replace the empty string at the end of the line $ with the file name.
Of course, your Awk script could easily be fixed, too. Standard Awk does not have an option to parallel the -i "in-place" option of sed, but you can easily use a temporary file:
for file in ./*.faa;
do
awk '/>/{ $0 = $0 " " FILENAME);sub(/\.faa/,"")}1' "$file" >"$file.tmp" &&
mv "$file.tmp" "$file"
done
GNU Awk also has an -i inplace extension which you could simply add to the options of your existing script if you have GNU Awk.
Since FASTA files typically contain multiple headers, adding to the header rather than replacing all headers in a file with the same string seems more useful, so I changed your Awk script to do that instead.
For what it's worth, the name of the character ^ is caret (carrot is 🥕). The character > is called greater than or right angle bracket, or right broket or sometimes just wedge.
You just need to detect the pattern to replace and use regex to implement it:
fasta_helper.sh
location=$1
for file in $location/*.faa
do
full_filename=${file##*/}
filename="${full_filename%.*}"
#scape special chars
filename=$(echo $filename | sed 's_/_\\/_g')
echo "adding file name: $filename to: $full_filename"
sed -i -E "s/^[^#]+/>$filename /" $location/$full_filename
done
usage:
Just pass the folder with fasta files:
bash fasta_helper.sh /foo/bar
test:
lectures
Regex: matching up to the first occurrence of a character
Extract filename and extension in Bash
https://unix.stackexchange.com/questions/78625/using-sed-to-find-and-replace-complex-string-preferrably-with-regex
Locating your files
Suggesting to first identify your files with find command or ls command.
find . -type f -name "*.faa" -printf "%f\n"
A find command to print only file with filenames extension .faa. Including sub directories to current directory.
ls -1 "*.faa"
An ls command to print files and directories with extension .faa. In current directory.
Processing your files
Once you have the correct files list, iterate over the list and apply sed command.
for fileName in $(find . -type f -name "*.faa" -printf "%f\n"); do
stripedFileName=${fileName/.*/} # strip extension .faa
sed -i "1s|\$| $stripedFileName|" "fileName" # append value of stripedFileName at end of line 1
done
This question already has answers here:
Rename multiple files based on pattern in Unix
(24 answers)
Closed 5 years ago.
Write a simple script that will automatically rename a number of files. As an example we want the file *001.jpg renamed to user defined string + 001.jpg (ex: MyVacation20110725_001.jpg) The usage for this script is to get the digital camera photos to have file names that make some sense.
I need to write a shell script for this. Can someone suggest how to begin?
An example to help you get off the ground.
for f in *.jpg; do mv "$f" "$(echo "$f" | sed s/IMG/VACATION/)"; done
In this example, I am assuming that all your image files contain the string IMG and you want to replace IMG with VACATION.
The shell automatically evaluates *.jpg to all the matching files.
The second argument of mv (the new name of the file) is the output of the sed command that replaces IMG with VACATION.
If your filenames include whitespace pay careful attention to the "$f" notation. You need the double-quotes to preserve the whitespace.
You can use rename utility to rename multiple files by a pattern. For example following command will prepend string MyVacation2011_ to all the files with jpg extension.
rename 's/^/MyVacation2011_/g' *.jpg
or
rename <pattern> <replacement> <file-list>
this example, I am assuming that all your image files begin with "IMG" and you want to replace "IMG" with "VACATION"
solution : first identified all jpg files and then replace keyword
find . -name '*jpg' -exec bash -c 'echo mv $0 ${0/IMG/VACATION}' {} \;
for file in *.jpg ; do mv $file ${file//IMG/myVacation} ; done
Again assuming that all your image files have the string "IMG" and you want to replace "IMG" with "myVacation".
With bash you can directly convert the string with parameter expansion.
Example: if the file is IMG_327.jpg, the mv command will be executed as if you do mv IMG_327.jpg myVacation_327.jpg. And this will be done for each file found in the directory matching *.jpg.
IMG_001.jpg -> myVacation_001.jpg
IMG_002.jpg -> myVacation_002.jpg
IMG_1023.jpg -> myVacation_1023.jpg
etcetera...
find . -type f |
sed -n "s/\(.*\)factory\.py$/& \1service\.py/p" |
xargs -p -n 2 mv
eg will rename all files in the cwd with names ending in "factory.py" to be replaced with names ending in "service.py"
explanation:
In the sed cmd, the -n flag will suppress normal behavior of echoing input to output after the s/// command is applied, and the p option on s/// will force writing to output if a substitution is made. Since a sub will only be made on match, sed will only have output for files ending in "factory.py"
In the s/// replacement string, we use "& " to interpolate the entire matching string, followed by a space character, into the replacement. Because of this, it's vital that our RE matches the entire filename. after the space char, we use "\1service.py" to interpolate the string we gulped before "factory.py", followed by "service.py", replacing it. So for more complex transformations youll have to change the args to s/// (with an re still matching the entire filename)
Example output:
foo_factory.py foo_service.py
bar_factory.py bar_service.py
We use xargs with -n 2 to consume the output of sed 2 delimited strings at a time, passing these to mv (i also put the -p option in there so you can feel safe when running this). voila.
NOTE: If you are facing more complicated file and folder scenarios, this post explains find (and some alternatives) in greater detail.
Another option is:
for i in *001.jpg
do
echo "mv $i yourstring${i#*001.jpg}"
done
remove echo after you have it right.
Parameter substitution with # will keep only the last part, so you can change its name.
Can't comment on Susam Pal's answer but if you're dealing with spaces, I'd surround with quotes:
for f in *.jpg; do mv "$f" "`echo $f | sed s/\ /\-/g`"; done;
You can try this:
for file in *.jpg;
do
mv $file $somestring_${file:((-7))}
done
You can see "parameter expansion" in man bash to understand the above better.
I have a folder with lots of files which name has the following structure:
01.artist_name - song_name.mp3
I want to go through all of them and rename them using the regexp:
/^d+\./
so i get only :
artist_name - song_name.mp3
How can i do this in bash?
You can do this in BASH:
for f in [0-9]*.mp3; do
mv "$f" "${f#*.}"
done
Use the Perl rename utility utility. It might be installed on your version of Linux or easy to find.
rename 's/^\d+\.//' -n *.mp3
With the -n flag, it will be a dry run, printing what would be renamed, without actually renaming. If the output looks good, drop the -n flag.
Use 'sed' bash command to do so:
for f in *.mp3;
do
new_name="$(echo $f | sed 's/[^.]*.//')"
mv $f $new_name
done
...in this case, regular expression [^.].* matches everything before first period of a string.
Sorry if this is very simple compared to usual questions but I am just starting out. I have some files all with the same start name but of different file types, e.g:
1234.x
1234.y
1234.z
1234_V2.x
1234_V2.y
1234_V2.z
I want to rename the first part of these whilst keeping any ending and file type, e.g:
4321.x
4321.y
4321.z
4321_V2.x etc
I have tried using
mv 1234* 4321*
and
rename 1234* 4321*
But no luck! I have also been through all the other SO articles and although I could use a loop, most depend on the file type being the same.
Thanks in advance
You can use bash substitution:
for file in 1234*
do mv "$file" "4321${file#1234}"
done
OR, replace the do mv with the following
do mv "$file" "${file/1234/4321}"
See more in man bash under EXPANSION section, sub-section Parameter Expansion
Assuming your filenames for 1234 and 4321 i.e constant for all files, you can try this
for fn in `find . -name 1234*`
do
newf=`echo $fn | sed s/1234/4321/`
mv $fn $newfn
done
You can use a shell script, but it's kind of ugly because it will fork a lot, and thus, if you have a lot of files to rename, it will take time.
for f in 1234*; do echo mv $f $(echo $f | sed -e 's/1234/4321/'); done
Otherwize, rename is a good way to do it:
rename 's/1234/4321/' 1234*
Rename expects a regular expression as first parameter, see online documentation
See if it works:
rename "s/1234/4321/" 1234*
command means substitute(because of s) occurances of "1234" with "4321" in files that has name of pattern 1234*
You can also look at here. It is slightly more complicated than your case.
I just downloaded about 600 files from my server and need to remove the last 11 characters from the filename (not including the extension). I use Ubuntu and I am searching for a command to achieve this.
Some examples are as follows:
aarondyne_kh2_13thstruggle_or_1250556383.mus should be renamed to aarondyne_kh2_13thstruggle_or.mus
aarondyne_kh2_darknessofunknow_1250556659.mp3 should be renamed to aarondyne_kh2_darknessofunknow.mp3
It seems that some duplicates might exist after I do this, but if the command fails to complete and tells me what the duplicates would be, I can always remove those manually.
Try using the rename command. It allows you to rename files based on a regular expression:
The following line should work out for you:
rename 's/_\d+(\.[a-z0-9A-Z]+)$/$1/' *
The following changes will occur:
aarondyne_kh2_13thstruggle_or_1250556383.mus renamed as aarondyne_kh2_13thstruggle_or.mus
aarondyne_kh2_darknessofunknow_1250556659.mp3 renamed as aarondyne_kh2_darknessofunknow.mp3
You can check the actions rename will do via specifying the -n flag, like this:
rename -n 's/_\d+(\.[a-z0-9A-Z]+)$/$1/' *
For more information on how to use rename simply open the manpage via: man rename
Not the prettiest, but very simple:
echo "$filename" | sed -e 's!\(.*\)...........\(\.[^.]*\)!\1\2!'
You'll still need to write the rest of the script, but it's pretty simple.
find . -type f -exec sh -c 'mv {} `echo -n {} | sed -E -e "s/[^/]{10}(\\.[^\\.]+)?$/\\1/"`' ";"
one way to go:
you get a list of your files, one per line (by ls maybe) then:
ls....|awk '{o=$0;sub(/_[^_.]*\./,".",$0);print "mv "o" "$0}'
this will print the mv a b command
e.g.
kent$ echo "aarondyne_kh2_13thstruggle_or_1250556383.mus"|awk '{o=$0;sub(/_[^_.]*\./,".",$0);print "mv "o" "$0}'
mv aarondyne_kh2_13thstruggle_or_1250556383.mus aarondyne_kh2_13thstruggle_or.mus
to execute, just pipe it to |sh
I assume there is no space in your filename.
This script assumes each file has just one extension. It would, for instance, rename "foo.something.mus" to "foo.mus". To keep all extensions, remove one hash mark (#) from the first line of the loop body. It also assumes that the base of each filename has at least 12 character, so that removing 11 doesn't leave you with an empty name.
for f in *; do
ext=${f##*.}
new_f=${base%???????????.$ext}
if [ -f "$new_f" ]; then
echo "Will not rename $f, $new_f already exists" >&2
else
mv "$f" "$new_f"
fi
done