I'm trying to build a script where a portion of it utilizes 'sed' to tag the filename onto the end of each line in that file, then dumps the output to a master list.
The part of the script giving me trouble is sed here:
DIR=/var/www/flatuser
FILES=$DIR/*
for f in $FILES
do
echo "processing $f file...."
sed -i "s/$/:$f/" $f
cat $f >> $DIR/master.txt
done
The issue is that the 'sed' statement works fine outside of the for loop, but when I place it in the script, I believe it's having issues interpreting the dollar signs. I've tried nearly every combo of " and ' that I can think of to get it to interpret the variable and it continuously either puts "$f" at the end of each line, or it fails outright.
Thanks for any input!
You just need to escape the dollar sign:
sed -i "s/\$/:$f/" "$f"
so that the shell passes it literally to sed.
To expand on Charles Duffy's point about quoting variables:
DIR=/var/www/flatuser
for f in "$DIR"/*
do
echo "processing $f file...."
sed -i "s/\$/:${f##*/}/" "$f"
cat "$f" >> "$DIR/master.txt"
done
If any file names contain a space, it's too late to do anything about it if you assign the list of file names to $FILES; you can no longer distinguish between spaces that belong to file names and spaces that separate file names. You could use an array instead, but it's simpler to just put the glob directly in the for loop. Here's how you would use an array:
DIR=/var/www/flatuser
FILES=( "$DIR"/* )
for f in "${FILES[#]}"
do
echo "processing $f file...."
sed -i "s/\$/:${f##*/}/" "$f"
cat "$f" >> "$DIR/master.txt"
done
For versions of sed that don't use -i, here's a way to explicitly handle the temp file needed to simulate in-place editing:
t=$(mktmp sXXXX); sed "s/\$/:$f/" "$f" > "$t"; mv "$t" "$f" && rm "$t"
Personally, I'd do this like so:
dir=/var/www/flatuser
for f in "$dir"/*; do
[[ $f = */master.txt ]] && continue
while read -r; do printf '%s:%s\n' "$REPLY" "${f##*/}"; done <"$f"
done >/var/www/flatuser/master.txt
It doesn't modify your files in-place the way sed -i does, so it's safe to run more than one time (the sed -i version will add the names to your files in-place every time it runs, so you'll end up with each line having more than one copy of the filename on it).
Also, sed -i isn't specified by POSIX, so not all operating systems will have it.
The problem is NOT the dollar sign. It's that the variable $f contains a "/" character, and sed is using that to separate expressions. Try using "#" as the separator.
DIR=/var/www/flatuser
FILES=$DIR/*
for f in $FILES
do
echo "processing $f file...."
sed -i s#"$"#:"$f"# $f
cat $f >> $DIR/master.txt
done
it's old, but maybe it helps someone.
Why not basename the file to get rid of leading directory
DIR=/var/www/flatuser
FILES=( "$DIR"/* )
for f in "${FILES[#]}"
do
echo "processing $f file...."
b=`basename $f`
sed -i "s/\$/:${b##*/}/" "$b"
cat "$f" >> "$DIR/master.txt"
done
not tested ...
Related
I want to be able to comment and uncomment lines which are "managed" using a bash script.
I am trying to write a script which will update all of the config lines which have the word #managed after them and remove the preceeding # if it exists.
The rest of the config file needs to be left unchanged. The config file looks like this:
configFile.txt
#config1=abc #managed
#config2=abc #managed
config3=abc #managed
config3=abc
This is the script I have created so far. It iterates the file, finds lines which contain "#managed" and detects if they are currently commented.
I need to then write this back to the file, how do I do that?
manage.sh
#!/bin/bash
while read line; do
STR='#managed'
if grep -q "$STR" <<< "$line"; then
echo "debug - this is managed"
firstLetter=${$line:0:1}
if [ "$firstLetter" = "#" ]; then
echo "Remove the initial # from this line"
fi
fi
echo "$line"
done < configFile.txt
With your approach using grep and sed.
str='#managed$'
file=ConfigFile.txt
grep -q "^#.*$str" "$file" && sed "/^#.*$str/s/^#//" "$file"
Looping through files ending in *.txt
#!/usr/bin/env bash
str='#managed$'
for file in *.txt; do
grep -q "^#.*$str" "$file" &&
sed "/^#.*$str/s/^#//" "$file"
done
In place editing with sed requires the -i flag/option but that varies from different version of sed, the GNU version does not require an -i.bak args, while the BSD version does.
On a Mac, ed should be installed by default, so just replace the sed part with.
printf '%s\n' "g/^#.*$str/s/^#//" ,p Q | ed -s "$file"
Replace the Q with w to actually write back the changes to the file.
Remove the ,p if no output to stdout is needed/required.
On a side note, embedding grep and sed in a shell loop that reads line-by-line the contents of a text file is considered a bad practice from shell users/developers/coders. Say the file has 100k lines, then grep and sed would have to run 100k times too!
This sed one-liner should do the trick:
sed -i.orig '/#managed/s/^#//' configFile.txt
It deletes the # character at the beginning of the line if the line contains the string #managed.
I wouldn't do it in bash (because that would be slower than sed or awk, for instance), but if you want to stick with bash:
#! /bin/bash
while IFS= read -r line; do
if [[ $line = *'#managed'* && ${line:0:1} = '#' ]]; then
line=${line:1}
fi
printf '%s\n' "$line"
done < configFile.txt > configFile.tmp
mv configFile.txt configFile.txt.orig && mv configFile.tmp configFile.txt
I am new with Bash, and trying to rename files in my folder keeping the first 9 characters intact and get rid of anything that comes after.
abc123456olda.jpg > abc123456.jpg
I wrote this;
for file in *
do
echo mv "$file" `echo "$file" | sed -e 's/(.{9}).*(\.jpg)$/$1$2/' *.jpg
done
Did not get it to work. Can someone guide what am I doing wrong?
You're not far off, try this:
for file in *.jpg; do
echo mv "$file" "$(echo "$file" | sed -E -e 's/(.{9}).*(\.jpg)$/\1\2/')"
done
There are some corrections. A important one is that $1$2 should be \1\2, and you need the -E flag to sed so that it understands the grouping with parenthesis.
Once you see the command is alright, remove the echo from the second line so mv actually gets executed.
Use bash's built-in parameter expansion operator rather than sed.
Also, you should put *.jpg in the for statement, not the sed argument; what you're doing is processing the contents of the files, not the filenames.
for file in *.jpg
do
mv "$file" "${file:0:9}.jpg"
done
${file:0:9} means the substring of $file starting from index 0 and having 9 characters.
I have a list of filenames like this in bash
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R1.fq.gz
UTSHoS10_Other_CAAGCC-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
UTSHoS11_Other_AGGCCT-TTAGGA_R_160418.R2.fq.gz
UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R1.fq.gz
UTSHoS12_Other_GGCAAG-TTAGGA_R_160418.R2.fq.gz
And I want them to look like this
UTSHoS10_R1.fq.gz
UTSHoS10_R2.fq.gz
UTSHoS11_R1.fq.gz
UTSHoS11_R2.fq.gz
UTSHoS12_R1.fq.gz
UTSHoS12_R2.fq.gz
I do not have the perl rename command and sed 's/_Other*160418./_/' *.gz
is not doing anything. I've tried other rename scripts on here but either nothing occurs or my shell starts printing huge amounts of code to the console and freezes.
This post (Removing Middle of Filename) is similar however the answers given do not explain what specific parts of the command are doing so I could not apply it to my problem.
Parameter expansions in bash can perform string substitutions based on glob-like patterns, which allows for a more efficient solution than calling an extra external utility such as sed in each loop iteration:
for f in *.gz; do echo mv "$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 $newname; done
Notes:
I've adjusted your sed command: it had an * without a preceeding . (sed takes a regular expression, not a globbing pattern). Similarly, the dot needs escaping.
To see if it works, without actually renaming the files, I've left the echo command in. Easy to remove just that to make it functional.
It doesn't have to be a one-liner, obviously. But sometimes, that makes editing and browsing your command-line history easier.
I would like to change lowercase filenames to uppercase with awk/sed/bash
your help would be appreciated
aaaa.txt
vvjv.txt
acfg.txt
desired output
AAAA.txt
VVJV.txt
ACFG.txt
PREFACE:
If you don't care about the case of your extensions, simply use the 'tr' utility in a shell loop:
for i in *.txt; do mv "$i" "$(echo "$i" | tr '[a-z]' '[A-Z]')"; done
If you do care about the case of the extensions, then you should be aware that there is more than one way to do it (TIMTOWTDI). Personally, I believe the Perl solution, listed here, is probably the simplest and most flexible solution under Linux. If you have multiple file extensions, simply specify the number you wish to keep unchanged. The BASH4 solution is also a very good one, but you must be willing to write out the extension a few times, or alternatively, use another variable to store it. But if you need serious portability then I recommend the last solution in this answer which uses octals. Some flavours of Linux also ship with a tool called rename that may also be worth checking out. It's usage will vary from distro to distro, so type man rename for more info.
SOLUTIONS:
Using Perl:
# single extension
perl -e 's/\.[^\.]*$/rename $_, uc($`) . $&/e for #ARGV' *.txt
# multiple extensions
perl -e 's/(?:\.[^\.]*){2}$/rename $_, uc($`) . $&/e for #ARGV' *.tar.gz
Using BASH4:
# single extension
for i in *.txt; do j="${i%.txt}"; mv "$i" "${j^^}.txt"; done
# multiple extensions
for i in *.tar.gz; do j="${i%.tar.gz}"; mv "$i" "${j^^}.tar.gz"; done
# using a var to store the extension:
e='.tar.gz'; for i in *${e}; do j="${i%${e}}"; mv "$i" "${j^^}${e}"; done
Using GNU awk:
for i in *.txt; do
mv "$i" $(echo "$i" | awk '{ sub(/.txt$/,""); print toupper($0) ".txt" }');
done
Using GNU sed:
for i in *.txt; do
mv "$i" $(echo "$i" | sed -r -e 's/.*/\U&/' -e 's/\.TXT$/\u.txt/');
done
Using BASH3.2:
for i in *.txt; do
stem="${i%.txt}";
for ((j=0; j<"${#stem}"; j++)); do
chr="${stem:$j:1}"
if [[ "$chr" == [a-z] ]]; then
chr=$(printf "%o" "'$chr")
chr=$((chr - 40))
chr=$(printf '\'"$chr")
fi
out+="$chr"
done
mv "$i" "$out.txt"
out=
done
In general for lowercase/upper case modifications "tr" ( translate characters ) utility is often used, it's from the set of command line utilities used for character replacement.
dtpwmbp:~ pwadas$ echo "xxx" | tr '[a-z]' '[A-Z]'
XXX
dtpwmbp:~ pwadas$
Also, for renaming files there's "rename" utility, delivered with perl ( man rename ).
SYNOPSIS
rename [ -v ] [ -n ] [ -f ] perlexpr [ files ]
DESCRIPTION
"rename" renames the filenames supplied according to the rule specified as the first argument. The perlexpr argument is a Perl expression which is expected to modify the $_ string in
Perl for at least some of the filenames specified. If a given filename is not modified by the expression, it will not be renamed. If no filenames are given on the command line,
filenames will be read via standard input.
For example, to rename all files matching "*.bak" to strip the extension, you might say
rename 's/\.bak$//' *.bak
To translate uppercase names to lower, you'd use
rename 'y/A-Z/a-z/' *
I would suggest using rename, if you only want to uppercase the filename and not the extension, use something like this:
rename -n 's/^([^.]*)\.(.*)$/\U$1\E.$2/' *
\U uppercases everything until \E, see perlreref(1). Remove the -n when your happy with the output.
Bash 4 parameter expansion can perform case changes:
for i in *.txt; do
i="${i%.txt}"
mv "$i.txt" "${i^^?}.txt"
done
bash:
for f in *.txt; do
no_ext=${f%.txt}
mv "$f" "${no_ext^^}.txt"
done
for f in *.txt; do
mv "$f" "`tr [:lower:] [:upper:] <<< "${f%.*}"`.txt"
done
An easier, lightweight and portable approach would be:
for i in *.txt
do
fname=$(echo $i | cut -d"." -f1 | tr [a-z] [A-Z])
ext=$(echo $i | cut -d"." -f2)
mv $i $fname.$ext
done
This would work on almost every version of BASH since we are using most common external utilities (cut, tr) found on every Unix flavour.
Simply use (on terminal):
for i in *.txt; do mv $i `echo ${i%.*} | tr [:lower:] [:upper:]`.txt; done;
This might work for you (GNU sed):
printf "%s\n" *.txt | sed 'h;s/[^.]*/\U&/;H;g;s/\(.*\)\n/mv -v \1 /' | sh
or more simply:
printf "%s\n" *.txt | sed 'h;s/[^.]*/\U&/;H;g;s/\(.*\)\n/mv -v \1 /e'
for i in *.jar; do mv $i `echo ${i%} | tr [:upper:] [:lower:]`; done;
this works for me.
I run a script which generated about 10k files in a directory. I just discovered that there is a bug in the script which causes some filenames to have a carriage return (presumably a '\n' character).
I want to run a sed command to remove the carriage return from the filenames.
Anyone knows which params to pass to sed to clean up the filenames in the manner described?
I am running Linux (Ubuntu)
I don't know how sed would do this, but this python script should do the trick:.
This isn't sed, but I find python a lot easier to use when doing things like these:
#!/usr/bin/env python
import os
files = os.listdir('.')
for file in files:
os.rename(file, file.replace('\r', '').replace('\n', ''))
print 'Processed ' + file.replace('\r', '').replace('\n', '')
It strips any occurrences of both \r and \n from all of the filenames in a given directory.
To run it, save it somewhere, cd into your target directory (with the files to be processed), and run python /path/to/the/file.py.
Also, if you plan on doing more batch renaming, consider Métamorphose. It's a really nice and powerful GUI for this stuff. And, it's free!
Good luck!
Actually, try this: cd into the directory, type in python, and then just paste this in:
exec("import os\nfor file in os.listdir('.'):\n os.rename(file, file.replace('\\r', '').replace('\\n', ''))\n print 'Processed ' + file.replace('\\r', '').replace('\\n', '')")
It's a one-line version of the previous script, and you don't have to save it.
Version 2, with space replacement powers:
#!/usr/bin/env python
import os
for file in os.listdir('.'):
os.rename(file, file.replace('\r', '').replace('\n', '').replace(' ', '_')
print 'Processed ' + file.replace('\r', '').replace('\n', '')
And here's the one-liner:
exec("import os\nfor file in os.listdir('.'):\n os.rename(file, file.replace('\\r', '').replace('\\n', '')replace(' ', '_'))\n print 'Processed ' + file.replace('\\r', '').replace('\\n', '');")
If there are no spaces in your filenames, you can do:
for f in *$'\n'; do mv "$f" $f; done
It won't work if the newlines are embedded, but it will work for trailing newlines.
If you must use sed:
for f in *$'\n'; do mv "$f" "$(echo "$f" | sed '/^$/d')"; done
Using the rename Perl script:
rename 's/\n//g' *$'\n'
or the util-linux-ng utility:
rename $'\n' '' *$'\n'
If the character is a return instead of a newline, change the \n or ^$ to \r in any places they appear above.
The reason you aren't getting any pure-sed answers is that fundamentally sed edits file contents, not file names; thus the answers that use sed all do something like echo the filename into a pipe (pseudo file), edit that with sed, then use mv to turn that back into a filename.
Since sed is out, here's a pure-bash version to add to the Perl, Python, etc scripts you have so far:
killpattern=$'[\r\n]' # remove both carriage returns and linefeeds
for f in *; do
if [[ "$f" == *$killpattern* ]]; then
mv "$f" "${f//$killpattern/}"
fi
done
...but since ${var//pattern/replacement} isn't available in plain sh (along with [[...]]), here's a version using sh-only syntax, and tr to do the character replacement:
for f in *; do
new="$(printf %s "$f" | tr -d "\r\n")"
if [ "$f" != "$new" ]; then
mv "$f" "$new"
fi
done
EDIT: If you really want it with sed, take a look at this:
http://www.linuxquestions.org/questions/programming-9/merge-lines-in-a-file-using-sed-191121/
Something along these lines should work similar to the perl below:
for i in *; do echo mv "$i" `echo "$i"|sed ':a;N;s/\n//;ta'`; done
With perl, try something along these lines:
for i in *; do mv "$i" `echo "$i"|perl -pe 's/\n//g'`; done
This will rename all files in the current folder by removing all newline characters from them. If you need to go recursive, you can use find instead - be aware of the escaping in that case, though.
In fact there is a way to use sed:
carr='\n' # specify carriage return
files=( $(ls -f) ) # array of files in current dir
for i in ${files[#]}
do
if [[ -n $(echo "$i" | grep $carr) ]] # filenames with carriage return
then
mv "$i" "$(echo "$i" | sed 's/\\n//g')" # move!
fi
done
This actually works.