I want to compare two folders(they both have the same zip files). I want to make sure they are exactly the same. How can i achieve that?
I tend to do a find on the directory, executing a checksum on each file within that directory. I sort the output and then do a final checksum on the sorted output. If the final checksum of each directory is the same, I think it is safe to assume they are the same.
The command I use is
find _dir_ -type f -exec cksum {} \; | sort | cksum
Hope this helps.
Related
I am trying to get the following done. I have circa 40 directories of different species, each with 100s of sequence files that contain orthologous sequences. The sequence files are similarly named for each of the species directories. I want to concatenate the identically named files of the 40 species directories into a single sequence file which is named similarly.
My data looks as follows, e.g.:
directories: Species1 Species2 Species3
Within directory (similar for all): sequenceA.fasta sequenceB.fasta sequenceC.fasta
I want to get single files named: sequenceA.fasta sequenceB.fasta sequenceC.fasta
where the content of the different files from the different species is concatenated.
I tried to solve this with a loop (but this never ends well with me!):
ls . | while read FILE; do cat ./*/"$FILE" >> ./final/"$FILE"; done
This resulted in empty files and errors. I did try to find a solution elsewhere, e.g.: (https://www.unix.com/unix-for-dummies-questions-and-answers/249952-cat-multiple-files-according-file-name.html, https://unix.stackexchange.com/questions/424204/how-to-combine-multiple-files-with-similar-names-in-different-folders-by-using-u) but I have been unable to edit them to my case.
Could anyone give me some help here? Thanks!
In a root directory where your species directories reside, you should run the following:
$ mkdir output
$ find Species* -type f -name "*.fasta" -exec sh -c 'cat {} >> output/`basename {}`' \;
It traverses all the files recursively and merges the contents of files with identical basename into one under output directory.
EDIT: even though this was an accepted answer, in a comment the OP mentioned that the real directories don't match a common pattern Species* as shown in the original question. In this case you can use this:
$ find -type f -not -path "./output/*" -name "*.fasta" -exec sh -c 'cat {} >> output/`basename {}`' \;
This way, we don't specify the search pattern but rather explicitly omit output directory to avoid duplicates of already processed data.
I searched all over for this, but the terms are apparently too general. I'm writing a script to search a group of folders for .mp3 files. Some folders don't have mp3's so they have to be excluded.
I created an array to hold the uniq'd folder names. This find command will get the folders I need.
Folders=$(sudo find /my/music/ -type f -name "*.mp3" | cut -d'/' -f7 | sort -u)
When I try to count the number of folders in the array, I always get 1
echo ${#Folders[#]}
echo ${Folders[#]} prints them out on separate lines so I thought they were separate array elements. Can anyone explain what is going on? You might have to jiggle the field number in the cut command to reproduce locally.
Folders is not an array but a variable.
You need:
Folders=( $(sudo find /my/music/ -type f -name "*.mp3" | cut -d'/' -f7 | sort -u) )
i.e. enclose the command substitution with (). Now ${#Folders[#]} would give you the number of elements of array Folders.
Or do :
sudo find /my/music/ -type f -name "*.mp3" | cut -d'/' -f7 | sort -u | wc -l
Note
wc -l prints the number of lines which in this case would be the number of unique files
to make things a bit more explicit, use -printf "%p\n" option with find where %p specifier prints the file with full path.
Assuming bash 4 or later, don't use find here; use the globstar operator.
shopt -s globstar
folders=( /my/music/**/*.mp3 )
Also assuming that cut -d/ -f7 is supposed to extract the filename alone, follow this up with
folders=${folders[#]##*/}
Other methods for populating the array must take more care to accomodate files containing whitespace or characters like ?, *, or [. File names containing newlines (rare, but not illegal) are much more difficult to handle correctly. Pathname expansion is done inside the shell, so you don't need to worry about any such special characters.
Lets say I am in /home/myuser
there are 90,000 files there inside 3000 directories.
How can I write a bash function or with linux commands to get one random file?
It could be C as well I suppose
You can list all your files and then pick a random line between them:
find /home/myuser | sort -R | head -n1
However this is not very efficient, and could take a while, but is easy to understand. You can work from here.
You can use shuf for this task, for example set globstar option and try
shuf -e path/**/*.txt | head -n1
Edit: I think this has been answered successfully, but I can't check 'til later. I've reformatted it as suggested though.
The question: I have a series of files, each with a name of the form XXXXNAME, where XXXX is some number. I want to move them all to separate folders called XXXX and have them called NAME. I can do this manually, but I was hoping that by naming them XXXXNAME there'd be some way I could tell Terminal (I think that's the right name, but not really sure) to move them there. Something like
mv *NAME */NAME
but where it takes whatever * was in the first case and regurgitates it to the path.
This is on some form of Linux, with a bash shell.
In the real life case, the files are 0000GNUmakefile, with sequential numbering. I'm having to make lots of similar-but-slightly-altered versions of a program to compile and run on a cluster as part of my research. It would probably have been quicker to write a program to edit all the files and put in the right place in the first place, but I didn't.
This is probably extremely simple, and I should be able to find an answer myself, if I knew the right words. Thing is, I have no formal training in programming, so I don't know what to call things to search for them. So hopefully this will result in me getting an answer, and maybe knowing how to find out the answer for similar things myself next time. With the basic programming I've picked up, I'm sure I could write a program to do this for me, but I'm hoping there's a simple way to do it just using functionality already in Terminal. I probably shouldn't be allowed to play with these things.
Thanks for any help! I can actually program in C and Python a fair amount, but that's through trial and error largely, and I still don't know what I can do and can't do in Terminal.
SO many ways to achieve this.
I find that the old standbys sed and awk are often the most powerful.
ls | sed -rne 's:^([0-9]{4})(NAME)$:mv -iv & \1/\2:p'
If you're satisfied that the commands look right, pipe the command line through a shell:
ls | sed -rne 's:^([0-9]{4})(NAME)$:mv -iv & \1/\2:p' | sh
I put NAME in brackets and used \2 so that if it varies more than your example indicates, you can come up with a regular expression to handle your filenames better.
To do the same thing in gawk (GNU awk, the variant found in most GNU/Linux distros):
ls | gawk '/^[0-9]{4}NAME$/ {printf("mv -iv %s %s/%s\n", $1, substr($0,0,4), substr($0,5))}'
As with the first sample, this produces commands which, if they make sense to you, can be piped through a shell by appending | sh to the end of the line.
Note that with all these mv commands, I've added the -i and -v options. This is for your protection. Read the man page for mv (by typing man mv in your Linux terminal) to see if you should be comfortable leaving them out.
Also, I'm assuming with these lines that all your directories already exist. You didn't mention if they do. If they don't, here's a one-liner to create the directories.
ls | sed -rne 's:^([0-9]{4})(NAME)$:mkdir -p \1:p' | sort -u
As with the others, append | sh to run the commands.
I should mention that it is generally recommended to use constructs like for (in Tim's answer) or find instead of parsing the output of ls. That said, when your filename format is as simple as /[0-9]{4}word/, I find the quick sed one-liner to be the way to go.
Lastly, if by NAME you actually mean "any string of characters" rather than the literal string "NAME", then in all my examples above, replace NAME with .*.
The following script will do this for you. Copy the script into a file on the remote machine (we'll call it sortfiles.sh).
#!/bin/bash
# Get all files in current directory having names XXXXsomename, where X is an integer
files=$(find . -name '[0-9][0-9][0-9][0-9]*')
# Build a list of the XXXX patterns found in the list of files
dirs=
for name in ${files}; do
dirs="${dirs} $(echo ${name} | cut -c 3-6)"
done
# Remove redundant entries from the list of XXXX patterns
dirs=$(echo ${dirs} | uniq)
# Create any XXXX directories that are not already present
for name in ${dirs}; do
if [[ ! -d ${name} ]]; then
mkdir ${name}
fi
done
# Move each of the XXXXsomename files to the appropriate directory
for name in ${files}; do
mv ${name} $(echo ${name} | cut -c 3-6)
done
# Return from script with normal status
exit 0
From the command line, do chmod +x sortfiles.sh
Execute the script with ./sortfiles.sh
Just open the Terminal application, cd into the directory that contains the files you want moved/renamed, and copy and paste these commands into the command line.
for file in [0-9][0-9][0-9][0-9]*; do
dirName="${file%%*([^0-9])}"
mkdir -p "$dirName"
mv "$file" "$dirName/${file##*([0-9])}"
done
This assumes all the files that you want to rename and move are in the same directory. The file globbing also assumes that there are at least four digits at the start of the filename. If there are more than four numbers, it will still be caught, but not if there are less than four. If there are less than four, take off the appropriate number of [0-9]s from the first line.
It does not handle the case where "NAME" (i.e. the name of the new file you want) starts with a number.
See this site for more information about string manipulation in bash.
I'm looking for examples of specifying files in a tree structure, for example, for specifying the set of files to search in a grep tool. I'd like to be able to include and exclude files and directories by name matches. I'm sure there are examples out there, but I'm having a hard time finding them.
Here's an example of a possible syntax:
*.py *.html
*.txt *.js
-*.pyc
-.svn/
-*combo_*.js
(this would mean include file with extensions .py .html .txt .js, exclude .pyc files, anything under a .svn directory, and any file matching combo_.js)
I know I've seen these sorts of specifications in other tools before. Is this ringing any bells for anyone?
There is no single standard format for this kind of thing, but if you want to copy something that is widely recognized, have a look at the rsync documentation. Look at the chapter on "INCLUDE/EXCLUDE PATTERN RULES."
Apache Ant provides 'ant globs or patterns where:
**/foo/**/*.java
means "any file ending in '.java' in a directory which includes a directory named 'foo' in its path" -- including ./foo/X.java
In your example syntax, is it implicitly understood that there's an escaping character so that you can explicitly include a file that begins with a dash? (The same question goes for any other wildcard characters, but I suppose I'd expect to see more files with dashes in their names than asterisks.)
Various command shells use * (and possibly ? to match a single char), as in your example, but they generally only match against a string of characters that doesn't include a path component separator (i.e. '\' on Windows systems, '/' elsewhere). I've also seen such source control apps as Perforce use additional patterns that can match against path component separators. For instance, with Perforce the pattern "foo/...ext" (without quotes) will match all files under the foo/ directory structure that end with "ext", regardless of whether they are in foo/ itself or in one of its descendant directories. This seems to be a useful pattern.
If you're using bash, you can use the extglob extension to get some nice globbing functions. Enable it as follows:
shopt -s extglob
Then you can do things like the following:
# everything but .html, .jpg or ,gif files
ls -d !(*.html|*gif|*jpg)
# list file9, file22 but not fileit
ls file+([0-9])
# begins with apl or un only
ls -d +(apl*|un*)
See also this page.
How about find in unixish environments?
Find can, of course, do more than build a list of files, but that is one of the common ways it is used. From the man page:
NAME
find -- walk a file hierarchy
SYNOPSIS
find [-H | -L | -P] [-EXdsx] [-f pathname] pathname ... expression
find [-H | -L | -P] [-EXdsx] -f pathname [pathname ...] expression
DESCRIPTION
The find utility recursively descends the directory tree for each
pathname listed, evaluating an expression (composed of the
primaries''
andoperands'' listed below) in terms of each file in the tree.
to achieve your goal I would write something like (formatted for readability):
find ./ \( -name *.{py,html,txt,js,pyc} -or \
-name *combo_*.js -or \
\( -name *.svn -and -type d\)\) \
-print
Moreover there is a idomatic pattern using xargs which makes find suitable for sending the whole list so constructed to an arbitrary command as in:
find /path -type f -print0 | xargs -0 rm
find(1) is a fine tool as described in the previous answer but if it gets more complicated, you should consider either writing your own script in any of the usual suspects (Ruby, Perl, Python et al.) or try to use one of the more powerful shells such as zsh which has a ** globbing commands and you can specify things to exclude. The latter is probably more complicated though.
You might want to check out ack, which allows you to specify file types to search in with options like --perl, etc.
It also ignores .svn directories by default, as well as core dumps, editor cruft, binary files, and so on.