I have several .vcf.gz files:
subset_file1.vcf.vcf.gz
subset_file2.vcf.vcf.gz
subset_file3.vcf.vcf.gz
I want to gunzip these file and rename them (remove subset_ and redudant .vcf extension in one go and get these files:
file1.vcf
file2.vcf
file3.vcf
This is the script I have tried:
iFILES=/file/path/*.gz
for i in $iFILES;
do gunzip -k $i > /get/in/this/dir/"${i##*/}"
done
Since you have to three operation at your output path name
1.remove the directory part
2.remove prefix subset_
3.remove redudant extension .vcf
It's hard to accomplish with only one command.
Following is a modification version. Be CAREFUL to try it. I didn't test it thorough in my computer.
for i in /file/path/*.gz;
do
# get the output file name
o=$(echo ${i##*/} | sed 's/.*_\(.*\)\(\.[a-z]\{3\}\)\{2\}.*/\1\2/g')
gunzip -k $i > /get/in/this/dir/$o
done
Related
I have a directory containing gzipped datafiles. I want to run each file using the script est_abundance.py. But first i need to unzip them. So i have this bash:
for file in /home/doy.user/scratch1/Secoutput/; do
cd "$file"
gunzip *kren.gz
python analysis1.py -i /Secoutput/*kren -k gkd_output -o /bracken_output/$(basename *kren).txt
wait
done
The problem is, the bash script keeps on unzipping all of the datafiles, it does not continue to the next command after unzipping one file.
Can you help me correct this? I just want every command to be done for every file.
Use, notice that you should use $file variable, and you can get the name of the file after unzipping by stripping the .gz part using ${file%.gz}:
for file in /home/doy.user/scratch1/Secoutput/*; do
gunzip $file
python analysis1.py -i ${file%.gz} -k gkd_output -o /bracken_output/$(basename ${file%.gz}).txt
wait
done
I need help copying content from various files to others (same name and format, different path).
For example, $HOME/initial/baby.desktop has text which I need to write into $HOME/scripts/baby.desktop. This is very simple for a single file, but I have 2500 files in $HOME/initial/ and the same number in $HOME/scripts/ with corresponding names (same names and format). I want append (copy) the content of file in path A to path B (which have the same name and format), to the end of file in path B without erase the content of file in path B.
Example content of $HOME/initial/*.desktop to final $HOME/scripts/*.desktop. I tried the following, but it don't work:
cd $HOME/initial/
for i in $( ls *.desktop ); do egrep "Icon" $i >> $HOME/scripts/$i; done
Firstly, I would backup $HOME/initial and $HOME/scripts, because there is lots of scope for people misunderstanding your question. Like this:
cd $HOME
tar -cvf initial.tar initial
tar -cvf scripts.tar scripts
That will put all the files in $HOME/initial into a single tarfile called initial.tar and all the files in $HOME/scripts into a single tarfile called scripts.tar.
Now for your question... in general, if you want to put the contents of FileB onto the end of FileA, the command is
cat FileB >> FileA
Note the DOUBLE ">>" which means "append" rather than single ">" which means overwrite.
So, I think you want to do this:
cd $HOME/initial/baby.desktop
cat SomeFile >> $HOME/scripts/baby.desktop/SomeFile
where SomeFile is the name of any file you choose to test with. I would test that has worked and then, if you are happy with that, go ahead and run the same command inside a loop:
cd $HOME/initial/baby.desktop
for SOURCE in *
do
DESTINATION="$HOME/scripts/baby.desktop/$SOURCE"
echo Appending "$SOURCE" to "$DESTINATION"
#cat "$SOURCE" >> "$DESTINATION"
done
When the output looks correct, remove the "#" at the start of the penultimate line and run it again.
I solved it, if some people want learn how to resolve is very simple:
using Sed
I need only the match (or pattern) line "Icon=/usr/share/some_picture.png into $HOME/initial/example.desktop to other with same name and format $HOME/scripts/example.desktop, but I had a lot of .desktop files (2500 files)
cd $HOME/initial
STRING_LINE=`grep -l -R "Icon=" *.desktop`
for i in $STRING_LINE; do sed -ne '/Icon=/ p' $i >> $HOME/scripts/$i ; done
_________
If you need only copy all to other file with same name and format
using cat
cd $HOME/initial
STRING_LINE=`grep -l -R "Icon=" *.desktop`
for i in $STRING_LINE; do cat $i >> $HOME/scripts/$i ; done
I want to write a script that do specific thing:
I have a txt file e.g.
from1/from2/from3/apple.file;/to1/to2/to3;some not important stuff
from1/from2/banana.file;/to1/to5;some not important stuff
from1/from10/plum.file;/to1//to5/to100;some not important stuff
Now i want to copy file from each line (e.g. apple.file), from original directory tree to new, non existing directories, after first semicolon (;).
I try few code examples from similar questions, but nothing works fine and I'm too weak in bash scripting, to find errors.
Please help :)
need to add some conditions:
file not only need to be copy, but also rename. Example line in file.txt:
from1/from2/from3/apple.file;to1/to2/to3/juice.file;some1
from1/from2/banana.file;to1/to5/fresh.file;something different from above
so apple.file need to be copy and rename to juice.file and put in to1/to2/to3/juice.file
I think thaht cp will also rename file but
mkdir -p "$to"
from answer below will create full folder path with juice.file as folder
In addidtion after second semicolon in each line will be something different, so how to cut it off?
Thanks for all help
EDIT: There will be no spaces in input txt file.
Try this code..
cat file | while IFS=';' read from to some_not_important_stuff
do
to=${to:1} # strip off leading space
mkdir -p "$to" # create parent for 'to' if not existing yet
cp -i "$from" "$to" # option -i to get a warning when it would overwrite something
done
Using awk
(run the awk command first and confirm the output is fine, then add |sh to do the copy)
awk -F";" '{printf "cp %s %s\n",$1,$2}' file |sh
Using shell (get updated that need manually create folder, base on alfe's
while IFS=';' read from to X
do
mkdir -p $to
cp $from $to
done < file
I had this same problem and used tar to solve it! Posted here:
tmpfile=/tmp/myfile.tar
files="/some/folder/file1.txt /some/other/folder/file2.txt"
targetfolder=/home/you/somefolder
tar --file="$tmpfile" "$files"
tar --extract --file="$tmpfile" --directory="$targetfolder"
In this case, tar will automatically create all (sub)folders for you! Best,
Nabi
I'm encountering many files with the same content and the same name on some of my servers. I need to quarantine these files for analysis so I can't just remove the duplicates. The OS is Linux (centos and ubuntu).
I enumerate the file names and locations and put them into a text file.
Then I do a for statement to move the files to quarantine.
for file in $(cat bad-stuff.txt); do mv $file /quarantine ;done
The problem is that they have the same file name and I just need to add something unique to the filename to get it to save properly. I'm sure it's something simple but I'm not good with regex. Thanks for the help.
Since you're using Linux, you can take advantage of GNU mv's --backup.
while read -r file
do
mv --backup=numbered "$file" "/quarantine"
done < "bad-stuff.txt"
Here's an example that shows how it works:
$ cat bad-stuff.txt
./c/foo
./d/foo
./a/foo
./b/foo
$ while read -r file; do mv --backup=numbered "$file" "./quarantine"; done < "bad-stuff.txt"
$ ls quarantine/
foo foo.~1~ foo.~2~ foo.~3~
$
I'd use this
for file in $(cat bad-stuff.txt); do mv $file /quarantine/$file.`date -u +%s%N`; done
You'll get everyfile with a timestamp appended (in nanoseconds).
You can create a new file name composed by the directory and the filename. Thus you can add one more argument in your original code:
for ...; do mv $file /quarantine/$(echo $file | sed 's:/:_:g') ; done
Please note that you should replace the _ with a proper character which is special enough.
I downloaded some files using wget and the files are in the following format:
test.zip?AWSAccesskeyId=XXXXXXX&Expires=00000000&Signature=ZZZZZZZZZZ
Is there any way, to rename those files properly by removing the URL parameters. Also is there any way, to download such files, with proper name(without URL parameter) from wget.
I tried with mmv with the following command:
mmv "*.zip*" "#1.zip"
But I can't find any way to install mmv. I am using CentOS 6. So, please suggest any way, other than this.
for file in *.zip\?*; do mv "$file" "${file%%\?*}"; done
As far as I can tell, there's no option to wget telling it not to include the query string in the local filename. You can use the -O option to specify an explicit filename, and fix the driver script to remove the query string itself.
for i in `ls *.zip?*`; do echo $i | cut -f 1 -d \? | xargs -n1 mv $i ; done
sorry to lazy to do checking for spaces in names right now. and unable to test. i don't have access to a bash based system at this moment in time.
If you have g++ >=4.9.2 then you can install rnm and do:
rnm -ns '/n/.zip' *.zip\?*
# /n/ expands to file name without extension.
Or
rnm -rs '/\.zip\?.*/.zip/' *.zip\?*