I transferred millions of generated SVG files from DOS to a Linux box and just realized that there is a ^# as the last character of each file (the DOS end of file character) which is giving an error when I try to display the SVG file in a browser.
In this question:
How can I remove the last character of the last line of a file?
Maroun gives the solution as:
sed '$ s/.$//' your_file
But when I modify it to look like this:
sed '$ s/.$//' *.SVG
or
find . -print | grep .SVG | sed '$ s/.$//'
It does not work.
I would also like to be able to specify that it should only delete the last character if it is the ^#.
Can someone please tell me what I am doing wrong or how to get this to work. The SVG files are in thousands of sub directories so I need to be able to make the change from top to bottom of the tree structure.
I'm guessing your first example isn't working because it's taking only the last file expanded by *.SVG. The second example (the one with the find command) fails because you're passing find's output to sed instead of the file contents.
Also, if you want to change the files' contents with sed, you need to use -i so the changes are performed "in place".
You could try this:
for file in *.SVG
do
sed -i '$ s/.$//' $file
done
Or:
find . -name "*.SVG" -exec sed -i '$ s/.$//' {} \;
Related
I have a directory with multiple fasta file named as followed:
BC-1_bin_1_genes.faa
BC-1_bin_2_genes.faa
BC-1_bin_3_genes.faa
BC-1_bin_4_genes.faa
etc. (about 200 individual files)
The fasta header look like this:
>BC-1_k127_3926653_6 # 4457 # 5341 # -1 # ID=2_6;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.697
I now want to add the filename to the header since I want to annotate the sequences for each file.I tried the following:
for file in *.faa;
do
sed -i "s/>.*/${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|\$| $stripedFileName|" "fileName" # append value of stripedFileName at end of line 1
done
I'm trying to use the sed command in terminal to replace a specific line in all my text files with a certain extension by a specific string:
sed -i.bak '35s/^.*$/5\) 1\-4/' fitting_file*.feedme
So I am trying to replace line 35 in each of these files with the string "5) 1-4". When I run an ls fitting_file*.feedme | wc -l command in this directory, I get 221 files. However, when I run the above sed command, it only edits the FIRST file in the order of ls fitting_file*.feedme. I know this because grep '5) 1-4' fitting_file*.feedme continually only returns the first file on the list after I run the replacement command. I also tried replacing fitting_file*.feedme with a space-separated list of a couple of these files in my sed command as a test, but it still only operated on the one I chose to list first. Why is this happening?
sed operates on a single stream. It essentially concats all the files together and treats that as a single stream. So it replaces the 35th line of the big concatenated stream.
To see this, make a 20 line file called A and a 20 line file called B. Apply your sed command as
sed -i.bak '35s/^.*$/5\) 1\-4/' A B
and you will see the 15th line of B replaced.
I think this should answer your direct question. As far how to get done what you like, I assume you've already figured out that wrapping your sed command in a for is one way to do it. :)
Try
Create a file containing your sed instruction like this
#!/bin/bash
sed -i.bak '35s/^.*$/5\) 1\-4/' $1
exit 0
and call it prog.sh. Next make it executable :
chmod u+x prog.sh
now you can solve your problem using
find . -name fitting_file\*.feedme -exec ./prog.sh {} \;
You could do all this on one line but frankly the number of escapes required is a bit much. Good luck.
To do what you're trying to do without using a shell loop is:
awk -i inplace -v inplace::suffix=.bak 'FNR==35{$0="5) 1-4"}1' fitting_file*.feedme
Note that unlike sed which can just count lines across all input files, awk has NR to track the number of records (lines by default) across all files and FNR for the same but just within the current file.
The above uses GNU awk for inplace editing just like GNU sed has -i for that. The default awk on MacOS is BSD awk, not GNU awk, but you should install GNU awk as it doesn't have all the bugs/quirks that BSD awk does and it has a ton of extremely useful extensions.
If you just want to use MacOS's awk then it'd be something like:
find . -name 'fitting_file*.feedme' -exec sh -c "\
awk 'FNR==35{\$0=\"5) 1-4\"}1' \"\$1\" > \"\$1.bak\" &&
mv -- \"\$1.bak\" \"\$1\"
" sh {} \;
which is obviously getting kinda complicated - I'd probably put the awk+mv script in a file to execute from sh -c or just resort to a shell loop myself if faced with that alternative (or a similar quoting nightmare with xargs)!
I have found some similar questions here but not this specific one and I do not want to break all my files. I have a list of files and I simply need to replace all spaces with underscores. I know this is a sed command but I am not sure how to generically apply this to every file.
I do not want to rename the files, just modify them in place.
Edit: To clarify, just in case it's not clear, I only want to replace whitespace within the files, file names should not be changed.
find . -type f -exec sed -i -e 's/ /_/g' {} \;
find grabs all items in the directory (and subdirectories) that are files, and passes those filenames as arguments to the sed command using the {} \; notation. The sed command it appears you already understand.
if you only want to search the current directory, and ignore subdirectories, you can use
find . -maxdepth 1 -type f -exec sed -i -e 's/ /_/g' {} \;
This is a 2 part problem. Step 1 is providing the proper sed command, 2 is providing the proper command to replace all files in a given directory.
Substitution in sed commands follows the form s/ItemToReplace/ItemToReplaceWith/pattern, where s stands for the substitution and pattern stands for how the operation should take place. According to this super user post, in order to match whitespace characters you must use either \s or [[:space:]] in your sed command. The difference being the later is for POSIX compliance. Lastly you need to specify a global operation which is simply /g at the end. This simply replaces all spaces in a file with underscores.
Substitution in sed commands follows the form s/ItemToReplace/ItemToReplaceWith/pattern, where s stands for the substitution and pattern stands for how the operation should take place. According to this super user post, in order to match whitespace characters you must use either just a space in your sed command, \s, or [[:space:]]. The difference being the last 2 are for whitespace catching (tabs and spaces), with the last needed for POSIX compliance. Lastly you need to specify a global operation which is simply /g at the end.
Therefore, your sed command is
sed s/ /_/g FileNameHere
However this only accomplishes half of your task. You also need to be able to do this for every file within a directory. Unfortunately, wildcards won't save us in the sed command, as * > * would be ambiguous. Your only solution is to iterate through each file and overwrite them individually. For loops by default should come equipped with file iteration syntax, and when used with wildcards expands out to all files in a directory. However sed's used in this manner appear to completely lose output when redirecting to a file. To correct this, you must specify sed with the -i flag so it will edit its files. Whatever item you pass after the -i flag will be used to create a backup of the old files. If no extension is passed (-i '' for instance), no backup will be created.
Therefore the final command should simply be
for i in *;do sed -i '' 's/ /_/g' $i;done
Which looks for all files in your current directory and echos the sed output to all files (Directories do get listed but no action occurs with them).
Well... since I was trying to get something running I found a method that worked for me:
for file in `ls`; do sed -i 's/ /_/g' $file; done
I would like to know how to search from the command line for a string in various files of type .rb.
And replace:
.delay([ANY OPTIONAL TEXT FOR DELETION]).
with
.delay.
Besides sed an awk are there any other command line tools included in the OS that are better for the task?
Status
So far I have the following regular expression:
.delay\(*.*\)\.
I would like to know how to match only the expression ending on the first closing parenthesis? And avoid replacing:
.delay([ANY OPTIONAL TEXT FOR DELETION]).sometext(param)
Thanks in advance!
If you need to find and replace text in files - sed seems to be the best command line solution.
Search for a string in the text file and replace:
sed -i 's/PATTERN/REPLACEMENT/' file.name
Or, if you need to process multiple occurencies of PATTERN in file, add g key
sed -i 's/PATTERN/REPLACEMENT/g' file.name
For multiple files processing - redirect list of files to sed:
echo "${filesList}" | xargs sed -i ...
You can use find to generate your list of files, and xargs to run sed over the result:
find . -type f -print | xargs sed -i 's/\.delay.*/.delay./'
find will generate a list of files contained in your current directory (., although you can of course pass a different directory), xargs will read that list and then run sed with the list of files as an argument.
Instead of find, which here generates a list of all files, you could use something like grep to generate a list of files that contain a specific term. E.g.:
grep -rl '\.delay' | xargs sed -i ...
For the part of the question where you want to only match and replace until the first ) and not include a second pair of (), here is how to change your regex:
.delay\(*.*\)\.
->
\.delay\([^\)]*\)
I.e. match "actual dot, delay, brace open, everything but brace close and brace close".
E.g. using sed:
>echo .delay([ANY OPTIONAL TEXT FOR DELETION]).sometext(param) | sed -E "s/\.delay\([^\)]*\)/.delay/"
.delay.sometext(param)
I recommend to use grep for finding the right files:
grep -rl --include "*.rb" '\.delay' .
Then feed the list into xargs, as recommended by other answers.
Credits to the other answers for providing a solution for feeding multiple files into sed.
I am trying to do a simple operation here. Which is to cut a few characters from one file (style.css) do a find a replace on another file (client_custom.css) for more then 100 directories with different names
When I use the following command
for d in */; do sed -n 73p ~/assets/*/style.css | cut -c 29-35 | xargs -I :hex: sed -i 's/!BGCOLOR!/:hex:/' ~/assets/*/client_custom.css $d; done
It keeps giving me the following error for all the directories
sed: couldn't edit dirname/: not a regular file
I am confused on why its giving me that error message explicitly gave the full path to the file. It works perfectly fine without a for loop.
Can anyone please help me out with this issue?
sed doesn't support folders as input.
for d in */;
puts folders into $d. If you write sed ... $d, then BASH will put the folder name into the arguments of sed and the poor tool will be confused.
Also ~/assets/*/client_custom.css since this will expand to all the files which match this pattern. So sed will be called once with all file names. You probably want to invoke sed once per file name.
Try
for f in ~/assets/*/client_custom.css; do
... | sed -i 's/!BGCOLOR!/:hex:/' $f
done
or, even better:
for f in ~/assets/*/client_custom.css; do
... | sed 's/!BGCOLOR!/:hex:/' "${f}.in" > "${f}"
done
(which doesn't overwrite the output file). This way, you can keep the "*.in" files, edit them with the patterns and then use sed to "expand" all the variables.