Looking for help with the following code. I have a folder titled data, with 6 subfolders (folder1, folder2, etc). Each folder has a text file I want to rename to "homeworknotes" keeping the .txt extension.
Used notes before for short:
So far I have the following code:
for file in data/*/*.txt; do
mv $file "notes"
done
find
You can use find command with -execdir that will execute command of your choice in a directory where file matching pattern is:
find data -type f -name '*.txt' -execdir mv \{\} notes.txt \;
data is path to directory where find should look for matching files recursively
-type f look only for files, not directories
-name '*.txt' match anything that ends with .txt
-execdir mv \{\} notes.txt run command mv {} notes.txt in directory where file was found; where {} is original filename found by find.
bash
EDIT1: To do this without find you need to handle recursive directory traversal (unless you have fixed directory layout). In bash you can set following shell options with shopt -s command:
extglob - extended globbing support (allows to write extended globs like **; see "Pathname Expansion" in man bash)
globstar - allows ** in pathname expansion; **/ will match any directories and their subdirectories (see "Pathname Expansion" in man bash).
nullglob - allows patterns that match no files (in case there's a directory without any .txt file)
Following script will traverse directories under data/ and rename .txt files to notes.txt:
#!/bin/bash
shopt -s extglob globstar nullglob
for f in data/**/*.txt ; do
mv $f $(dirname $f)/notes.txt
done
mv $f $(dirname $f)/notes.txt moves (renames) file; $f contains matched path so e.g. data/folder1/day4notes.txt and $(dirname $f) gets directory where that file is - in this case data/folder1 so we just append /notes.txt to that.
EDIT2: If you are absolutely positive that you want to do this only in first level of subdirectories under data/ you can omit extglob and globstar (and if you know there's at least one .txt in each directory then also nullglob) and go ahead with pattern you posted; but you still need to use mv $f $(dirname $f)/notes.txt to rename file.
NOTE: When experimenting with things like these always make backup beforehand. If you have multiple .txt files in any of directories they all will get renamed to notes.txt so you might lose data in that case.
I would like to batch copy specific files that ends with fastq.gz from each folder (with unique names) to a new directory, but it keeps giving me an error saying that the files cannot be found. Is it because I am using a wildcard wrong?
for f in ./*/split-adapter-quality-trimmed/*.fastq.gz; do
cp *fastq.gz ../../new;
done
Executing for f in ./*/split-adapter-quality-trimmed/*.fastq.gz will already contain the filenames ending with *.fastq.gz in variable f. So use it directly in cp (cp $f destination) inside the loop. If you put an echo $f inside the loop, you can see all the files and verify it before cp.
for f in ./*/split-adapter-quality-trimmed/*.fastq.gz; do
cp $f ../../new;
done
Except if you absolutely want to use a for-loop, you could perform that with one find command:
find ./*/split-adapter-quality-trimmed -name "*fastq.gz" -exec cp {} ../../new \;
It will browse the directories matching ./*/split-adapter-quality-trimmed, looking for each file terminating with fastq.gz, and then execute the needed cp command (in the current directory of the shell, the command line ends with a semi-colon):
cp <found-path> ../../new
(The wildcarded term *fastq.gz is surrounded by quotes to prevent Bash to interpret it, just in case. So is it with the semi-colon.)
I was trying to rename some files to another extension:
# mv *.sqlite3_done *.sqlite3
but got an error:
mv: target '*.sqlite3' is not a directory
Why?
the easy way is use find
find . -type f -name '*.sqlite3_done' -exec sh -c 'x="{}"; mv "$x" "${x%_done}"' \;
mv can only move multiple files into a single directory; it can’t move each one to a different name. You can loop in bash instead:
for x in *.sqlite3_done; do
mv -- "$x" "${x%_done}"
done
${x%_done} removes _done from the end of $x.
The wildcard expansion results in multiple names being passed to the command. The shell thinks you are trying to move multiple files to the *.sqlite3 directory.
You need to use a loop:
for nam in *sqlite3_done
do
newname=${nam%_done}
mv $nam $newname
done
The %_done says to remove the last occurrence of _done from the string.
If you may have spaces in your filenames you will want to quote the filenames.
From the current directory I have multiple sub directories:
subdir1/
001myfile001A.txt
002myfile002A.txt
subdir2/
001myfile001B.txt
002myfile002B.txt
where I want to strip every character from the filenames before myfile so I end up with
subdir1/
myfile001A.txt
myfile002A.txt
subdir2/
myfile001B.txt
myfile002B.txt
I have some code to do this...
#!/bin/bash
for d in `find . -type d -maxdepth 1`; do
cd "$d"
for f in `find . "*.txt"`; do
mv "$f" "$(echo "$f" | sed -r 's/^.*myfile/myfile/')"
done
done
however the newly renamed files end up in the parent directory
i.e.
myfile001A.txt
myfile002A.txt
myfile001B.txt
myfile002B.txt
subdir1/
subdir2/
In which the sub-directories are now empty.
How do I alter my script to rename the files and keep them in their respective sub-directories? As you can see the first loop changes directory to the sub directory so not sure why the files end up getting sent up a directory...
Your script has multiple problems. In the first place, your outer find command doesn't do quite what you expect: it outputs not only each of the subdirectories, but also the search root, ., which is itself a directory. You could have discovered this by running the command manually, among other ways. You don't really need to use find for this, but supposing that you do use it, this would be better:
for d in $(find * -maxdepth 0 -type d); do
Moreover, . is the first result of your original find command, and your problems continue there. Your initial cd is without meaningful effect, because you're just changing to the same directory you're already in. The find command in the inner loop is rooted there, and descends into both subdirectories. The path information for each file you choose to rename is therefore stripped by sed, which is why the results end up in the initial working directory (./subdir1/001myfile001A.txt --> myfile001A.txt). By the time you process the subdirectories, there are no files left in them to rename.
But that's not all: the find command in your inner loop is incorrect. Because you do not specify an option before it, find interprets "*.txt" as designating a second search root, in addition to .. You presumably wanted to use -name "*.txt" to filter the find results; without it, find outputs the name of every file in the tree. Presumably you're suppressing or ignoring the error messages that result.
But supposing that your subdirectories have no subdirectories of their own, as shown, and that you aren't concerned with dotfiles, even this corrected version ...
for f in `find . -name "*.txt"`;
... is an awfully heavyweight way of saying this ...
for f in *.txt;
... or even this ...
for f in *?myfile*.txt;
... the latter of which will avoid attempts to rename any files whose names do not, in fact, change.
Furthermore, launching a sed process for each file name is pretty wasteful and expensive when you could just use bash's built-in substitution feature:
mv "$f" "${f/#*myfile/myfile}"
And you will find also that your working directory gets messed up. The working directory is a characteristic of the overall shell environment, so it does not automatically reset on each loop iteration. You'll need to handle that manually in some way. pushd / popd would do that, as would running the outer loop's body in a subshell.
Overall, this will do the trick:
#!/bin/bash
for d in $(find * -maxdepth 0 -type d); do
pushd "$d"
for f in *.txt; do
mv "$f" "${f/#*myfile/myfile}"
done
popd
done
You can do it without find and sed:
$ for f in */*.txt; do echo mv "$f" "${f/\/*myfile/\/myfile}"; done
mv subdir1/001myfile001A.txt subdir1/myfile001A.txt
mv subdir1/002myfile002A.txt subdir1/myfile002A.txt
mv subdir2/001myfile001B.txt subdir2/myfile001B.txt
mv subdir2/002myfile002B.txt subdir2/myfile002B.txt
If you remove the echo, it'll actually rename the files.
This uses shell parameter expansion to replace a slash and anything up to myfile with just a slash and myfile.
Notice that this breaks if there is more than one level of subdirectories. In that case, you could use extended pattern matching (enabled with shopt -s extglob) and the globstar shell option (shopt -s globstar):
$ for f in **/*.txt; do echo mv "$f" "${f/\/*([!\/])myfile/\/myfile}"; done
mv subdir1/001myfile001A.txt subdir1/myfile001A.txt
mv subdir1/002myfile002A.txt subdir1/myfile002A.txt
mv subdir1/subdir3/001myfile001A.txt subdir1/subdir3/myfile001A.txt
mv subdir1/subdir3/002myfile002A.txt subdir1/subdir3/myfile002A.txt
mv subdir2/001myfile001B.txt subdir2/myfile001B.txt
mv subdir2/002myfile002B.txt subdir2/myfile002B.txt
This uses the *([!\/]) pattern ("zero or more characters that are not a forward slash"). The slash has to be escaped in the bracket expression because we're still inside of the pattern part of the ${parameter/pattern/string} expansion.
Maybe you want to use the following command instead:
rename 's#(.*/).*(myfile.*)#$1$2#' subdir*/*
You can use rename -n ... to check the outcome without actually renaming anything.
Regarding your actual question:
The find command from the outer loop returns 3 (!) directories:
.
./subdir1
./subdir2
The unwanted . is the reason why all files end up in the parent directory (that is .). You can exclude . by using the option -mindepth 1.
Unfortunately, this was onyl the reason for the files landing in the wrong place, but not the only problem. Since you already accepted one of the answers, there is no need to list them all.
a slight modification should fix your problem:
#!/bin/bash
for f in `find . -maxdepth 2 -name "*.txt"`; do
mv "$f" "$(echo "$f" | sed -r 's,[^/]+(myfile),\1,')"
done
note: this sed uses , instead of / as the delimiter.
however, there are much faster ways.
here is with the rename utility, available or easily installed wherever there is bash and perl:
find . -maxdepth 2 -name "*.txt" | rename 's,[^/]+(myfile),/$1,'
here are tests on 1000 files:
for `find`; do mv 9.176s
rename 0.099s
that's 100x as fast.
John Bollinger's accepted answer is twice as fast as the OPs, but 50x as slow as this rename solution:
for|for|mv "$f" "${f//}" 4.316s
also, it won't work if there is a directory with too many items for a shell glob. likewise any answers that use for f in *.txt or for f in */*.txt or find * or rename ... subdir*/*. answers that begin with find ., on the other hand, will also work on directories with any number of items.
I have a directory that include several folders. I want to write a shell script to find a file in another directory that has the same name as the mentioned folders.
To clarify I have a directory that include test1 and test2 folders. I have another directory that have two files with the names of test1 and test2. My goal is to go to the directory that have folders and then get the folder names. Then by using folder name find the file that has the same name and copy it to that folder that has the same name.
I wrote the following script but it could not copy the file.
for d in /home/Documents/test/*/ ; do
find /home/Documents/binaries/ -name "$d" -type f -exec cp {} /home/Documents/test/$d \;
cd "$d"
done
$d will be set to a full path name, such as /home/Documents/test/test1/, but you only need test1 as the argument for the -name primary. You can use parameter expansion to strip the leading path from the value of $d, but it will take two steps.
for d in /home/Documents/test/*/ ; do
fname=${d##*/} # Strip /home/Documents/test/
fname=${fname%/} # Strip the trailing /
# Note that d is already the full directory name you want to use
# as the target file for `cp`
find /home/Documents/binaries/ -name "$fname" -type f -exec cp {} "$d" \;
done
The cd command doesn't seem to accomplish anything useful, since you are using absolute path names throughout.
Simpler, though, would be to change the working directory to /home/Documents/test first.
cd /home/Documents/test/
for d in */; do
find /home/Documents/binaries/ -name "$d" -type f -exec cp {} /home/Documents/test/"$d" \;
done