Im trying to move multiple files from one directory to another directory.
File name is with sequence and will be varying.
Example:
/global/userhome/usrsats/---------directory which has file names as below:
fl_cl_filename1
fl_cl_filename2
fl_cl_filename3
...
...
Now when moved to another directory, i need to get only the file name and delimit the fl_cl part.
Please help
Assuming you're using bash, I would do this with the remove the matching prefix pattern facility like this (with DEST_DIR set to the destination directory):
cd /global/userhome/usrsats
for f in *; do mv $f ${DEST_DIR}/${f#fl_cl_}; done
Related
I want to replace a constant string in multiple files based on the name of the file.
Example:
In a directory I have many files named like 'X-A01', 'X-B01', 'X-C01'.
In each file there is a string 'SS-S01'.
I want to replace string 'SS-S01' in the first file with 'X-A01', second file with 'X-B01' and third file with 'X-C01'.
Please help me how can we do it as I have hundreds of files like this and do not want to manually edit all files one by one.
Remember to back up your files(!) before running this command, since I have not actually tried it myself:
You could do something like:
for file in <DIR>/*; do sed -i "s/SS-S01/${file##*/}/" "$file"; done
This will loop over each file in <DIR> and for each loop iteration assign the file name to $file. For each file, sed will replace the first occurence of SS-S01 in that file by the file name.
I'm writing a unix shell script that sorts data in ten subdirectories (labelled 1-10) of the home directory. In each subdirectory, the script needs to rename the files hehd.output and fort.hehd.time, as well as copy the file hehd.data to a .data file with a new name.
What I'd like it to do is rename each of these files in the following format:
AA.BB.CC
Where
AA = a variable in the hehd.data file within the subdirectory containing the file
BB = the name of the subdirectory containing the file (1-10)
CC = the original file name
Each subdirectory contains an hehd.data file, and each hehd.data file contains the string ij0=AA, where AA represents the variable I want to use to rename the files in the same subdirectory.
For example: When run, the script should search /home/4/hehd.data for the string ij0=2, then move /home/4/hehd.output to /home/4/2.4.hehd.output.
I'm currently using the grep command to have the script search for the string ij0=* and copy it to a new text file within the subdirectory. Next, the string ij0= is deleted from the text file, and then its contents are used to rename all target files in the same subdirectory. The last line of the shell script deletes the text file.
I'm looking for a better way to accomplish this, preferably such that all ten subdirectories can be sorted at once by the same script. My script seems incredibly inefficient, and doesn't do everything that I want it to by itself.
How can I improve this?
Any advice or suggestions would be appreciated; I'm trying to become a better computer user and that means learning better ways of doing things.
Try this:
fromdir=/home
for i in {1..10};do
AA=$(sed 's/ij0=\([0-9]*\)/\1/' "$fromdir/$i/hehd.data")
BB="$i"
for f in "$fromdir/$i/"*;do
CC="${f##*/}"
if [[ "$CC" = "hehd.data" ]]; then
echo cp "$f" "$fromdir/$i/$AA.$BB.$CC"
else
echo mv "$f" "$fromdir/$i/$AA.$BB.$CC"
fi
done
done
It loops over directories using Bash sequence {1..10].
In each directory, with the sed command the ij0 value is assigned to AA variable, the directory name is assigned to BB.
In the file loop, if the file is hehd.data it's copied, else it's renamed with the new name.
You can remove the echo before cp and mv commands if the output meets your needs.
I have a folder of data folders with the following structure:
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/data1.gz
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/data2.gz
sampleName2-randomNumbers/subfolder1/subfolder2/subfolder3/data1.gz
I want to modify all the data.gz within each sample folder by appending the sample name but not the random numbers to get:
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/sampleName1_data1.gz
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/sampleName1_data2.gz
sampleName2-randomNumbers/subfolder1/subfolder2/subfolder3/sampleName2_data1.gz
It seems like this should be a simple mv for loop but I haven't been able to figure out how to pull part of a folder name using basename.
for i in */Data/Intensities/BaseCalls/*.gz; do mv $i "fastq""/"${i%%-*}"."`basename $i`; done
I couldn't figure out how to make the files stay in their original folder but for my purposes it works to have all the files go to a new folder ("fastq")
I suppose the "sampleName" part doesn't include dashes. In that case, use the standard pattern removal expansion: %%. That is, suppose your full path (relative to directory root) is stored in $path, just do ${path%%-*} to extract the "sampleName" part. Search for %% in the Bash Reference Manual for more details. As a simple example:
> path=sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/data1.gz
> echo ${path%%-*}
sampleName1
Otherwise, you could also use more advanced substring extraction based on regex. See BashFAQ/100 or Manipulating Strings from the TLDP Advanced Bash Scripting Guide.
Update. Here's the full command to perform the job described, and it is entirely native to the shell:
for file in */Data/Intensities/BaseCalls/*.gz; do
mv "$file" "${file%/*}/${file%%-*}_${file##*/}"
done
I have 312 directories labeled,
Ion_0001- Ion_0312.
In each directory I have a file light.out. I'd like to change the file names in each directory to, for example:
Ion_0001.out
I believe I also need to substitute the / so that my output DOESNT look this this:
Ion_0001/.out
Can any one help me out with a simple script??
This is what I've tried:
#!/bin/bash
for dir in */
do
cd $dir
for filename in *.out; do
mv $filename ${filename//$dir.out}
done
cd ..
done
Thanks!
Not a free coding service, but it's simple enough to not make it worth arguing about...
Assuming this file structure:
Ion_0001/
Ion_0001/light.out
Ion_0002/
Ion_0002/light.out
...
Run this code in a script or just at the command line:
for i in Ion_0*
do
mv "${i}/light.out" "${i}/${i}.out"
done
Resulting in this structure:
Ion_0001/
Ion_0001/Ion_0001.out
Ion_0002/
Ion_0002/Ion_0002.out
...
Is that what you were looking for?
for dir in Ion*/; do
mv "${dir}light.out" "${dir}${dir%/}.out"
done
The trailing slash in the Ion*/ pattern limits the results to directories only, but the slash will be present in the variable's value.
I'm not very good in shell scripting and would like to ask you some question about looping of files big dataset: in my example I have alot of files with the common .pdb extension in the work dir. I need to loop all of them and i) to print name (w.o pdb extension) of each looped file and make some operation after this. E.g I need to make new dir for EACH file outside of the workdir with the name of each file and copy this file to that dir. Below you can see example of my code which are not worked- it's didn't show me the name of the file and didn't create folder for each of them. Please correct it and show me where I was wrong
#!/bin/bash
# set the work dir
receptors=./Receptors
for pdb in $receptors
do
filename=$(basename "$pdb")
echo "Processing of $filename file"
cd ..
mkdir ./docking_$filename
done
Many thanks for help,
Gleb
If all your files are contained within the .Repectors folder, you can loop each of them like so:
#!/bin/bash
for pdb in ./Receptors/*.pdb ; do
filename=$(basename "$pdb")
filenamenoextention=${filename/.pdb/}
mkdir "../docking_${filenamenoextention}"
done
Btw:
filenamenoextention=${filename/.pdb/}
Does a search replace in the variable $pdb. The syntax is ${myvariable/FOO/BAR}, and replaces all "FOO" substrings in $myvariable with "BAR". In your case it replaces ".pdb" with nothing, effectively removing it.
Alternatively, and safer (in case $filename contains multiple ".pdb"-substrings) is to remove the last four characters, like so: filenamenoextention=${filename:0:-4}
The syntax here is ${myvariable:s:e} where s and e correspond to numbers for the start and end index (not inclusive). It also let's you use negative numbers, which are offsets from the end. In other words: ${filename:0:-4} says: extract the substring from $filename starting from index 0, until you reach fourth-to-the-last character.
A few problems you have had with your script:
for pdb in ./Receptors loops only "./Receptors", and not each of the files within the folder.
When you change to parent directory (cd ..), you do so for the current shell session. This means that you keep going to the parent directory each time. Instead, you can specify the parent directory in the mkdir call. E.g mkdir ../thedir
You're looping over a one-item list, I think what you wanted to get is the list of the content of ./Receptors:
...
for pdb in $receptors/*
...
to list only file with .pdb extension use $receptors/*.pdb
So instead of just giving the path in for loop, give this:
for pdb in $receptors/*.pdb
To remove the extension :
set the variable ext to the extension you want to remove and using shell expansion operator "%" remove the extension from your filename eg:
ext=.pdb
filename=${filename%${ext}}
You can create the new directory without changing your current directory:
So to create a directory outside your current directory use the following command
mkdir ../docking_$filename
And to copy the file in the new directory use cp command
After correction
Your script should look like:
receptors=./Receptors
ext=.pdb
for pdb in $receptors/*.pdb
do
filename=$(basename "$pdb")
filename=${filename%${ext}}
echo "Processing of $filename file"
mkdir ../docking_$filename
cp $pdb ../docking_$filename
done