This question already has answers here:
Are shell scripts sensitive to encoding and line endings?
(14 answers)
Closed 1 year ago.
I am trying to write a bash script that takes 2 inputs: a list of IDs and 2) a directory. The idea is that the script will move a subset of files corresponding to the list of IDs into a a new folder.
#! /usr/bin/bash
LIST_FILE=$(cat ${1}) # List of file IDs (example entry: 1.2345)
PATH=${2} # directory name (i.e group_1)
for i in ${LIST_FILE}
do
/usr/bin/mv /tmp/project/project_data/data_all/${i}.annotated.gz /tmp/project/project_data/${PATH}/
done
The script manages to loop ok, however I get the following error for each iteration:
/usr/bin/mv: cannot stat '/tmp/project/project_data/data_all/1.2345'$'\r''.annotated.gz': No such file or directory
It looks like the file name hasn't concatenated properly and I'm not sure why. I've tried researching the problem but I'm also quite new to bash and finding it hard to grasp the concept of the stat error. I appreciate any advice and possible solutions.
Thanks everyone.
I think that the file whose name you pass as the first argument to your script is in dos format instead of unix so you are getting extra \r characters in your file names.
You could change your third line to:
LIST_FILE=$(cat ${1}|tr -d '\r')
Bobby
Related
This question already has answers here:
Are shell scripts sensitive to encoding and line endings?
(14 answers)
Read a file line by line assigning the value to a variable [duplicate]
(10 answers)
Closed 2 months ago.
New to coding
I have a very simple loop that Im using to rename files, but it stops after the first iteration.
Im running the loop:
for x in `cat list_genomes.txt`
do
mv -v $x"_busco/run_hypocreales_odb10" "/busco_runs/run_"$x
done
and the error I get is:
‘FV25228_busco/run_hypocreales_odb10’ -> ‘busco_runs/run_FV25228’
mv: cannot stat ‘\r_busco/run_hypocreales_odb10’: No such file or directory
mv: cannot stat ‘FV32968\r_busco/run_hypocreales_odb10’: No such file or directory
mv: cannot stat ‘FV34765\r_busco/run_hypocreales_odb10’: No such file or directory
mv: cannot stat ‘FV-NC-01\r_busco/run_hypocreales_odb10’: No such file or directory
so the first line works, but then it cannot read the rest.
list_genomes.txt looks like:
FV25228
FV32968
FV34765
FV-NC-01
Fc25332
Your input file has originated on a system that is not identical to the one where you are running the script.
The "\r" on the 2nd-5th line indicate that the file came from a Windows-based system. The person who created the file should have chosen a format that is compatible with system on which the data was going to be processed, which in this case appears to be Unix/Linux based.
If the creator of your input file doesn't change the way they do that, you need to massage the file before feeding it to your program logic, using the command dos2unix.
The following would likely provide you with the necessary fix if all else is correct:
#!/bin/bash
dos2unix -n list_genomes.txt list_genomes.fix
while read line
do
mv -v "${line}_busco/run_hypocreales_odb10" "/busco_runs/run_${line}"
done < list_genomes.fix
This question already has answers here:
Are shell scripts sensitive to encoding and line endings?
(14 answers)
Closed 1 year ago.
I am trying to paste two files together
file ip.txt
10.32.216.15
10.23.134.8
10.33.2.37
10.33.84.20
10.33.17.38
file obj.txt
obj-10.32.216.15
obj-10.23.134.8
obj-10.33.2.37
obj-10.33.84.20
obj-10.33.17.38
and I use the command like this:
paste ip.txt obj.txt
However I get this truncated output:
10.32.21obj-10.32.216.15
10.23.13obj-10.23.134.8
10.33.2.obj-10.33.2.37
10.33.84obj-10.33.84.20
10.33.17obj-10.33.17.38
The two files are created by grep command in my script earlier. This behavior is also present when I used variables with the command.
Also when I try to specify a delimiter only the second file gets pasted.
Does anyone know what might be the issue? Thanks
The issue was with line endings, for some reason Windows were set up but Unix were needed.
This question already has answers here:
Bash script to find and display oldest file
(4 answers)
Closed 2 years ago.
I'm looking for a BASH command (or set of commands) that will look in a specific directory and delete ONLY the single oldest file in that directory. I've looked around, but I can't quite find what I'm looking for. Hopefully someone can help me with this, because it's the last missing piece in my script. Everything else is working perfectly.
One way to delete oldest file ending with .specific :
rm -i $(ls -tr *.specific | sed q)
This is not very reliable if you have spaces in filenames
This question already has answers here:
"~/Desktop/test.txt: No such file or directory"
(2 answers)
Why isn't tilde (~) expanding inside double quotes? [duplicate]
(1 answer)
Closed 4 years ago.
I'm new to Linux as well as bash. I made a script that accesses a folder that is located in the home directory, but the script will not always be called from the home directory. The prompt I'm getting when calling it from any subdirectories specifies that it can not find the file.
Here's an example of what I'm trying to do:
for entry in "~/.directory"/*
do
echo "$entry"
done
If I place the script in a subdirectory of /home and try to call it, the script is unable to find the directory. I know it exists as if I run ls ~/.directory in the subdirectory it is able to find the files and print them with no problem. Is there a different way I should be trying to access the directory in the bash shell? Thanks!
Voted to close my question. It seems rather specific to me, and the general solution was something I found earlier and was also posted in the comments below. I'll figure it out eventually -
Only unquoted tildes are expanded.
for entry in ~/".directory"/*
This question already has an answer here:
Why would a correct shell script give a wrapped/truncated/corrupted error message? [duplicate]
(1 answer)
Closed 7 years ago.
I have 100 ".txt" files. Each file contains the data such as
File name Data
1.txt BAP1
2.txt UCHL1
3.txt ABC1234
Now I want to scan content of these files and write to txt file with condition that it contains my input string such as "BAP1". I used below coded but the output files have mistaken such as '1.txt .' I have no idea why the extension file has more dot in last file. Could you help me solve it? I am working in cygwin
#!/bin/sh
grep -w 'BAP1' *.txt>"1.txt"
grep -w 'UCHL1' *.txt>"2.txt"
Run dos2unix on your script, or otherwise tell your editor to save it as a UNIX text file.
Otherwise, your filenames will have carriage returns (aka $'\r') on the end of their names.