I want to store output of ls command in my bash script in a variable and use each file name in a loop, but for example one file in the directory has name "Hello world", when I do variable=$(ls) "Hello" and "world" end up as two separate entries, and when I try to do
for i in $variable
do
mv $i ~
done
it shows error that files "Hello" and "world" doesn't exist.
Is there any way I can access all files in current directory and run some command even if the files have space(s) in their names.
If you must, dirfiles=(/path/of/interest/*).
And accept the admonition against parsing the output of ls!
I understand you are new to this and I'd like to help. But it isn't easy for me (us?) to provide you with an answer that would be of much help to you by the way you've stated your question.
Based on what I hear so far, you don't seem to have a basic understanding on how parameter expansions work in the shell. The following two links will be useful to you:
Matching Pathnames, Parameters
Now, if your task at hand is to operate on files meeting certain criteria then find(1) will likely to do the job.
Say it with me: don't parse the output of ls! For more information, see this post on Unix.SE.
A better way of doing this is:
for i in *
do
mv -- "$i" ~
done
or simply
mv -- * ~
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 made a shell script the purpose of which is to find files that don't contain a particular string, then display the first line that isn't empty or otherwise useless. My script works well in the console, but for some reason when I try to direct the output to a .txt file, it comes out empty.
Here's my script:
#!/bin/bash
# takes user input.
echo "Input substance:"
read substance
echo "Listing media without $substance:"
cd media
# finds names of files that don't feature the substance given, then puts them inside an array.
searchresult=($(grep -L "$substance" *))
# iterates the array and prints the first line of each - contains both the number and the medium name.
# however, some files start with "Microorganisms" and the actual number and name feature after several empty lines
# the script checks for that occurence - and prints the first line that doesnt match these criteria.
for i in "${searchresult[#]}"
do
grep -m 1 -v "Microorganisms\|^$" $i
done >> output.txt
I've tried moving the >>output.txt to right after the grep line inside the loop, tried switching >> to > and 2>&1, tried using tee. No go.
I'm honestly feeling utterly stuck as to what the issue could be. I'm sure there's something I'm missing, but I'm nowhere near good enough with this to notice. I would very much appreciate any help.
EDIT: Added files to better illustrate what I'm working with. Sample inputs I tried: Glucose, Yeast extract, Agar. Link to files [140kB] - the folder was unzipped beforehand.
The script was given full permissions to execute. I don't think the output is being rewritten because even if I don't iterate and just run a single line of the loop, the file is empty.
I'am new in Linux and I want to write a bash script that can read in a file name of a directory that starts with LED + some numbers.(Ex.: LED5.5.002)
In that directory there is only one file that will starts with LED. The problem is that this file will every time be updated, so the next time it will be for example LED6.5.012 and counting.
I searched and tried a little bit and came to this solution:
export fspec=/home/led/LED*
LedV=`basename $fspec`
echo $LedV
If I give in those commands one by one in my terminal it works fine, LedV= LED5.5.002 but if i run it in a bash scripts it gives the result: LedV = LED*
I search after another solution:
a=/home/led/LED*
LedV=$(basename $a)
echo $LedV
but here again the same, if i give it in one by one it's ok but in a script: LedV = LED*.
It's probably something small but because of my lack of knowledge over Linux I cannot find it. So can someone tell what is wrong?
Thanks! Jan
Shell expansions don't happen on scalar assignments, so in
varname=foo*
the expansion of "$varname" will literally be "foo*". It's more confusing when you consider that echo $varname (or in your case basename $varname; either way without the double quotes) will cause the expansion itself to be treated as a glob, so you may well think the variable contains all those filenames.
Array expansions are another story. You might just want
fspec=( /path/LED* )
echo "${fspec[0]##*/}" # A parameter expansion to strip off the dirname
That will work fine for bash. Since POSIX sh doesn't have arrays like this, I like to give an alternative approach:
for fspec in /path/LED*; do
break
done
echo "${fspec##*/}"
pwd
/usr/local/src
ls -1 /usr/local/src/mysql*
/usr/local/src/mysql-cluster-gpl-7.3.4-linux-glibc2.5-x86_64.tar.gz
/usr/local/src/mysql-dump_test_all_dbs.sql
if you only have 1 file, you will only get 1 result
MyFile=`ls -1 /home/led/LED*`
I'm trying to redirect(?) my standard error/output to a text file.
I did my research, but for some reason the online answers are not working for me.
What am I doing wrong?
cd /home/user1/lists/
for dir in $(ls)
do
(
echo | $dir > /root/user1/$dir" "log.txt
) > /root/Desktop/Logs/Update.log
done
I also tried
2> /root/Desktop/Logs/Update.log
1> /root/Desktop/Logs/Update.log
&> /root/Desktop/Logs/Update.log
None of these work for me :(
Help please!
Try this for the basics:
echo hello >> log.txt 2>&1
Could be read as: echo the word hello, redirecting and appending STDOUT to the file log.txt. STDERR (file descriptor 2) is redirected to wherever STDOUT is being pointed. Note that STDOUT is the default and thus there is no "1" in front of the ">>". Works on the current line only.
To redirect and append all output and error of all commands in a script, put this line near the top. It will be in effect for the length of the script instead of doing it on each line:
exec >>log.txt 2>&1
If you are trying to obtain a list of the files in /home/user1/lists, you do not need a loop at all:
ls /home/usr1/lists/ >Update.log
If you are attempting to run every file in the directory as an executable with a newline as its input, and collect the output from all these programs in Update.log, try this:
for file in /home/user1/lists/*; do
echo | "$file"
done >Update.log
(Notice how we avoid the useless use of ls and how there is no redirection inside the loop.)
If you want to create an empty file called *.log.txt for each file in the directory, you would do
for file in /home/user1/lists/*; do
touch "$(basename "$file")"log.txt
done
(Using basename to obtain the file name without the directory part avoids the cd but you could do it the other way around. Generally, we tend to avoid changing the directory in scripts, so that the tool can be run from anywhere and generate output in the current directory.)
If you want to create a file containing a single newline, regardless of whether it already exists or not,
for file in /home/user1/lists/*; do
echo >"$(basename "$file")"log.txt
done
In your original program, you redirect the echo inside the loop, which means that the redirection after done will not receive any output at all, so the created file will be empty.
These are somewhat wild guesses at what you might actually be trying to accomplish, but should hopefully help nudge you slightly in the right direction. (This should properly be a comment, I suppose, but it's way too long and complex.)