I have files in directories like:
./PBMCs/SRR1_1.fastq
./PBMCs/SRR1_2.fastq
./Monos/SRR2.fastq
./Monos/SRR3.fastq
I want to change the SRR# to a more informative name based on a file of key-value pairs:
SRR1 pbmc-1
SRR2 mono-1
SRR3 mono-2
And rename the files as:
./PBMCs/pbmc-1_1.fastq
./PBMCs/pbmc-1_2.fastq
./Monos/mono-1.fastq
./Monos/mono-2.fastq
All that I can think to do is loop through the list of original files and then loop through the lines of the name-change.txt file and replace the strings. However, I'm not sure how to implement this or if it's a good way to approach this.
Assuming all *.fastq are one subdirectory deep, this should work fine:
while read old new; do
for fastq in ./*/"$old"*.fastq; do
new_name=$new${fastq##*/"$old"}
echo mv "$fastq" "${fastq%/*}/$new_name"
done
done <name-change.txt
Remove echo if the output looks good.
Related
I need to combine all the csv files in some directory (.csv), provided that there are other files with the same name in this directory, but with different expansion (.csv.done).
If a csv file doesn't have .done in this extension then I don't need it for combine process.
What is the best way to do it using Bash ?
This approach is a solution to your problem. I see you've commented that it "didn't work", but whatever the reason is for it not working, it's likely simple to fix e.g. if you forgot to include key details, or failed to adapt it appropriately to suit your specific situation. If you need further help troubleshooting, add more info to your question.
The approach:
for f in *.csv.done
do
cat "${f%.*}" >> combined_file.csv
done
How it works:
In your example, you have 3 files named 1.csv 2.csv 3.csv and two 'done' files named 1.csv.done 2.csv.done.
This script begins by making a list of all files that end in .csv.done (two files: 1.csv.done 2.csv.done).
It then uses a parameter expansion, specifically ${parameter%word}, to 'shorten' the name of the two files in the list to .csv (instead of .csv.done).
Then it 'prints' the content of the two 'shortened' filenames (1.csv and 2.csv) into a 'combined' file.
It doesn't 'print' the content of 1.csv.done or 2.csv.done, or 3.csv, because these files weren't in the original 'list'.
If you run this script multiple times, it will keep adding the contents of files 1.csv and 2.csv to the 'combined' file (only run it once, or delete the 'combined' file before running it again)
I am trying to iterate over files in a folder, renaming them as foldername1, foldername2, etc. However, I'm getting an error which says that the mv isn't being used correctly.
So far my code looks like this:
FILES='(Full Path)/Macbeth/audio/'
for file in "$FILES"*
do
mv $file 'Macbeth'$i''
done
The final code should iterate through the files and rename them as, in this case Macbeth1.mp3, but I'm not sure how the Bash syntax works.
As suggested by Cyrus, the solution was to use the full path
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'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