I have thousands of two set of files one with name.ext and another files name ending with name.ext.in, so for every name.ext there is a name.ext.in and now i have to pass this as argument to a script such as customise.pl name.ext name.ext.in. I am doing like
#!/bin/bash
FILE1=$.ext
FILE2=$.ext.in
customise.pl $FILE1 $FILE2
but no success. Any idea?
for i in *.ext; do
customise.pl "$i" "$i.in"
done
Judging from the comments to the other answers, you probably want something like this:
for file in *.ext; do
customise.pl "$file" "${file%.*}.new.psl"
done
The ${file%.*} syntax substitutes only the part of $file up until its last dot. You can check the manpages for Bash or Dash for more information on it if you need.
If you want to run customise.pl for each pair of files, you can do it like this in a bash script:
#!/bin/bash
for i in `ls *.ext`
do
customise.pl $i $i.in
done
I guess the simplest form is
for f in "*.ext"
do
customise.pl $f.ext $f.ext.in
done
OUTPUT:
another way.
ls *.ext |xargs -i customise.pl {} {}.in
Related
I have a list of filenames like this in bash
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R1.fq.gz
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R1.fq.gz
UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R2.fq.gz
And I want them to look like this
UTSHoS10_R1.fq.gz
UTSHoS10_R2.fq.gz
UTSHoS11_R1.fq.gz
UTSHoS11_R2.fq.gz
UTSHoS12_R1.fq.gz
UTSHoS12_R2.fq.gz
I do not have the perl rename command and sed 's/_Other*160418./_/' *.gz
is not doing anything. I've tried other rename scripts on here but either nothing occurs or my shell starts printing huge amounts of code to the console and freezes.
This post (Removing Middle of Filename) is similar however the answers given do not explain what specific parts of the command are doing so I could not apply it to my problem.
Parameter expansions in bash can perform string substitutions based on glob-like patterns, which allows for a more efficient solution than calling an extra external utility such as sed in each loop iteration:
for f in *.gz; do echo mv "$f" "${f/_Other_*-TTAGGA_R_160418./_}"; done
Remove the echo before mv to perform actual renaming.
You can do something like this in the directory which contains the files to be renamed:
for file_name in *.gz
do
new_file_name=$(sed 's/_[^.]*\./_/g' <<< "$file_name");
mv "$file_name" "$new_file_name";
done
The pattern (_[^.]*\.) starts matching from the FIRST _ till the FIRST . (both inclusive). [^.]* means 0 or more non-dot (or non-period) characters.
Example:
AMD$ ls
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R1.fq.gz UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R1.fq.gz
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R2.fq.gz UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
AMD$ for file_name in *.gz
> do new_file_name=$(sed 's/_[^.]*\./_/g' <<< "$file_name")
> mv "$file_name" "$new_file_name"
> done
AMD$ ls
UTSHoS10_R1.fq.gz UTSHoS10_R2.fq.gz UTSHoS11_R2.fq.gz UTSHoS12_R1.fq.gz UTSHoS12_R2.fq.gz
Pure Bash, using substring operation and assuming that all file names have the same length:
for file in UTS*.gz; do
echo mv -i "$file" "${file:0:9}${file:38:8}"
done
Outputs:
mv -i UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R1.fq.gz UTSHoS10_R1.fq.gz
mv -i UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R2.fq.gz UTSHoS10_R2.fq.gz
mv -i UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz UTSHoS11_R2.fq.gz
mv -i UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz UTSHoS11_R2.fq.gz
mv -i UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R1.fq.gz UTSHoS12_R1.fq.gz
mv -i UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R2.fq.gz UTSHoS12_R2.fq.gz
Once verified, remove echo from the line inside the loop and run again.
Going with your sed command, this can work as a bash one-liner:
for name in UTSH*fq.gz; do newname=$(echo $name | sed 's/_Other.*160418\./_/'); echo mv $name $newname; done
Notes:
I've adjusted your sed command: it had an * without a preceeding . (sed takes a regular expression, not a globbing pattern). Similarly, the dot needs escaping.
To see if it works, without actually renaming the files, I've left the echo command in. Easy to remove just that to make it functional.
It doesn't have to be a one-liner, obviously. But sometimes, that makes editing and browsing your command-line history easier.
I have the following files in the following format:
$ ls CombinedReports_LLL-*'('*.csv
CombinedReports_LLL-20140211144020(Untitled_1).csv
CombinedReports_LLL-20140211144020(Untitled_11).csv
CombinedReports_LLL-20140211144020(Untitled_110).csv
CombinedReports_LLL-20140211144020(Untitled_111).csv
CombinedReports_LLL-20140211144020(Untitled_12).csv
CombinedReports_LLL-20140211144020(Untitled_13).csv
CombinedReports_LLL-20140211144020(Untitled_14).csv
CombinedReports_LLL-20140211144020(Untitled_15).csv
CombinedReports_LLL-20140211144020(Untitled_16).csv
CombinedReports_LLL-20140211144020(Untitled_17).csv
CombinedReports_LLL-20140211144020(Untitled_18).csv
CombinedReports_LLL-20140211144020(Untitled_19).csv
I would like this part removed:
20140211144020 (this is the timestamp the reports were run so this will vary)
and end up with something like:
CombinedReports_LLL-(Untitled_1).csv
CombinedReports_LLL-(Untitled_11).csv
CombinedReports_LLL-(Untitled_110).csv
CombinedReports_LLL-(Untitled_111).csv
CombinedReports_LLL-(Untitled_12).csv
CombinedReports_LLL-(Untitled_13).csv
CombinedReports_LLL-(Untitled_14).csv
CombinedReports_LLL-(Untitled_15).csv
CombinedReports_LLL-(Untitled_16).csv
CombinedReports_LLL-(Untitled_17).csv
CombinedReports_LLL-(Untitled_18).csv
CombinedReports_LLL-(Untitled_19).csv
I was thinking simply along the lines of the mv command, maybe something like this:
$ ls CombinedReports_LLL-*'('*.csv
but maybe a sed command or other would be better
rename is part of the perl package. It renames files according to perl-style regular expressions. To remove the dates from your file names:
rename 's/[0-9]{14}//' CombinedReports_LLL-*.csv
If rename is not available, sed+shell can be used:
for fname in Combined*.csv ; do mv "$fname" "$(echo "$fname" | sed -r 's/[0-9]{14}//')" ; done
The above loops over each of your files. For each file, it performs a mv command: mv "$fname" "$(echo "$fname" | sed -r 's/[0-9]{14}//')" where, in this case, sed is able to use the same regular expression as the rename command above. s/[0-9]{14}// tells sed to look for 14 digits in a row and replace them with an empty string.
Without using an other tools like rename or sed and sticking strictly to bash alone:
for f in CombinedReports_LLL-*.csv
do
newName=${f/LLL-*\(/LLL-(}
mv -i "$f" "$newName"
done
for f in CombinedReports_LLL-* ; do
b=${f:0:20}${f:34:500}
mv "$f" "$b"
done
You can try line by line on shell:
f="CombinedReports_LLL-20140211144020(Untitled_11).csv"
b=${f:0:20}${f:34:500}
echo $b
You can use the rename utility for this. It uses syntax much like sed to change filenames. The following example (from the rename man-page) shows how to remove the trailing '.bak' extension from a list of backup files in the local directory:
rename 's/\.bak$//' *.bak
I'm using the advice given in the top response and have put the following line into a shell script:
ls *.nii | xargs rename 's/[f_]{2}//' f_0*.nii
In terminal, this line works perfectly, but in my script it will not execute and reads * as a literal part of the file name.
I would like to traverse through some directories that contain xml files. To each file I would like to apply an awk command and write the output to the file again. The file that is written is empty, though. Why? I use the following script:
#!/bin/bash
for f in `find /myDir/ -iname "*.xml"`
do
awk '/<string name="my\/ attribute" optional="false">/,/<\/string>/ {sub(/<value>(.*)<\/value>/,"<value>none</value>")}1' $f >$f
done
You must use a temporary file:
awk ... "$f" > "$f".tmp; mv "$f".tmp "$f"
The problem is not in awk, the problem is in the redirection. It is not possible to write to the file you are reading.
I am trying to create a small Bash script to remove hyphens from a filename. For example, I want to rename:
CropDamageVO-041412.mpg
to
CropDamageVO041412.mpg
I'm new to Bash, so be gentle :] Thank you for any help
Try this:
for file in $(find dirWithDashedFiles -type f -iname '*-*'); do
mv $file ${file//-/}
done
That's assuming that your directories don't have dashes in the name. That would break this.
The ${varname//regex/replacementText} syntax is explained here. Just search for substring replacement.
Also, this would break if your directories or filenames have spaces in them. If you have spaces in your filenames, you should use this:
for file in *-*; do
mv $file "${file//-/}"
done
This has the disadvantage of having to be run in every directory that contains files you want to change, but, like I said, it's a little more robust.
FN=CropDamageVO-041412.mpg
mv $FN `echo $FN | sed -e 's/-//g'`
The backticks (``) tell bash to run the command inside them and use the output of that command in the expression. The sed part applies a regular expression to remove the hyphens from the filename.
Or to do this to all files in the current directory matching a certain pattern:
for i in *VO-*.mpg
do
mv $i `echo $i | sed -e 's/-//g'`
done
A general solution for removing hyphens from any string:
$ echo "remove-all-hyphens" | tr -d '-'
removeallhyphens
$
f=CropDamageVO-041412.mpg
echo "${f//-}"
or, of course,
mv "$f" "${f//-}"
I have a folder full of text files. I need to append the same block of text to each of them (and of course overwrite the original file).
I was wondering what the correct Bash shell syntax would be for this. Would I use cat?
I have done a few batch scripts but I'm not a Bash expert. Any suggestions appreciated.
Use append redirection.
for f in *.txt
do
cat footer >> "$f"
done
If you're needing to do this via a script, you can use echo and append redirection to get the extra text into the files.
FILES=pathto/*
for f in $FILES ; do
echo "#extra text" >> $f
done
sed -i.bak "$ a $(<file_block_of_text)" *.txt
Variant of kurumi's answer:
sed -i.bak "\$aTEXTTOINSERT" *.txt
For more details, see SED: insert something to the last line?
very simply one which worked well for me
#!/bin/sh
FILES="./files/*"
for f in $FILES
do
echo '0000000' | cat - $f > temp && mv temp $f
done