file edit- commandline unix - linux

I want to edit a file from the command line, because opening it in vim or other editors takes forever (a large file). I want to add a string ('chr') to the beginning of every line that is not commented out with a #. The command I am using is this:
cat '/home/me/37.vcf' | sed s/^/chr/>'sp.vcf'
But it adds a chr to the beginning of EVERY line and a > to the END of every line. I don't want either of those things to occur.
Can anyone offer any suggestions to improve my results?

To apply the substitution to only the lines that don't start with a #:
sed '/^[^#]/s/^/chr/' file > output
Note: the command cat is for concatenating files, it is useless here.

You can syntax error in your sed command. Use this syntactically correct sed command:
sed -E 's/^([^#]|$)/chr/' /home/me/37.vcf > sp.vcf
OR on Linux:
sed -r 's/^([^#]|$)/chr/' /home/me/37.vcf > sp.vcf

This might work for you (GNU sed):
sed '/^\s*#/!s/^/chr/' file > new_file

Related

use sed to delete patterns on a range of lines

I have a large text file that I would like to divide into segments and use sed to delete certain patterns in place. I would like to do this in a single command line using a pipe. For example:
sed -n 1,10p <text file> | sed -i 's/<pattern to remove>//'
The code above attempts to take the first 10 lines of the text file and remove the patterns from the 10 lines in place. The resulting text file should have the first 10 lines modified. The code above doesn't work because the second command after the pipe requires a input file. Please help!
Something like
sed -i '1,10s/pattern//' foo.txt
though for in place editing of a file I prefer ed or perl instead of relying on a non standard sed extension like -i.
This seems to do what you're asking ....
sed -ni '1,10s/pattern//p' file

remove \n and keep space in linux

I have a file contained \n hidden behind each line:
input:
s3741206\n
s2561284\n
s4411364\n
s2516482\n
s2071534\n
s2074633\n
s7856856\n
s11957134\n
s682333\n
s9378200\n
s1862626\n
I want to remove \n behind
desired output:
s3741206
s2561284
s4411364
s2516482
s2071534
s2074633
s7856856
s11957134
s682333
s9378200
s1862626
however, I try this:
tr -d '\n' < file1 > file2
but it goes like below without space and new line
s3741206s2561284s4411364s2516482s2071534s2074633s7856856s11957134s682333s9378200s1862626
I also try sed $'s/\n//g' -i file1 and it doesn't work in mac os.
Thank you.
This is a possible solution using sed:
sed 's/\\n/ /g'
with awk
awk '{sub(/\\n/,"")} 1' < file1 > file2
What you are describing so far in your question+comments doesn't make sense. How can you have a multi-line file with a hidden newline character at the end of each line? What you show as your input file:
s3741206\n
s2561284\n
s4411364\n
etc.
where each "\n" above according to your comment is a single newline character "\n" is impossible. If those "\n"s were newline characters then your file would simply look like:
s3741206
s2561284
s4411364
etc.
There's really only 2 possibilities I can think of:
You are wrongly interpreting what you are seeing in your input file
and/or using the wrong terminology and you actually DO have \r\n
at the end of every line. Run cat -v file to see the \rs as
^Ms and run dos2unix or similar (e.g. sed 's/\r$//' file) to
remove the \rs - you do not want to remove the \ns or you will
no longer have a POSIX text file and so POSIX tools will exhibit
undefined behavior when run on it. If that doesn't work for you then
copy/paste the output of cat -v file into your question so we can
see for sure what is in your file.
Or:
It's also entirely possible that your file is a perfectly fine POSIX
text file as-is and you are incorrectly assuming you will have a
problem for some reason so also include in your question a
description of the actual problem you are having, include an example
of the command you are executing on that input file and the output
you are getting and the output you expected to get.
You could use bash-native string substitution
$ cat /tmp/newline
s3741206\n
s2561284\n
s4411364\n
s2516482\n
s2071534\n
s2074633\n
s7856856\n
s11957134\n
s682333\n
s9378200\n
s1862626\n
$ for LINE in $(cat /tmp/newline); do echo "${LINE%\\n}"; done
s3741206
s2561284
s4411364
s2516482
s2071534
s2074633
s7856856
s11957134
s682333
s9378200
s1862626

find matching text and replace next line

I'm trying to find a line in a file and replace the next line with a specific value. I tried sed, but it seems to not like the \n. How else can this be done?
The file looks like this:
<key>ConnectionString</key>
<string>anything_could_be_here</string>
And I'd like to change it to this
<key>ConnectionString</key>
<string>changed_value</string>
Here's what I tried:
sed -i '' "s/<key>ConnectionString<\/key>\n<string><\/string>/<key>ConnectionString<\/key>\n<string>replaced_text<\/string>/g" /path/to/file
One way:
Sample file
$ cat file
Cygwin
Unix
Linux
Solaris
AIX
Using sed, replacing the next line after the pattern 'Unix' with 'hi':
$ sed '/Unix/{n;s/.*/hi/}' file
Cygwin
Unix
hi
Solaris
AIX
For your specific question:
$ sed '/<key>ConnectionString<\/key>/{n;s/<string>.*<\/string>/<string>NEW STRING<\/string>/}' your_file
<key>ConnectionString</key>
<string>NEW STRING</string>
This might work for you (GNU sed):
sed '/<key>ConnectionString<\/key>/!b;n;c<string>changed_value</string>' file
!b negates the previous address (regexp) and breaks out of any processing, ending the sed commands, n prints the current line and then reads the next into the pattern space, c changes the current line to the string following the command.
It works. Additionaly is interested to mention that if you write,
sed '/<key>ConnectionString<\/key>/!b;n;n;c<string>changed_value</string>' file
Note the two n's, it replaces after two lines and so forth.

sed -e 's/^M/d' not working

A very common problem, but I am unable to work around it with sed.
I have a script file ( a batch of commands) say myfile.txt to be executed at once to create a list. Now when I am executing a batch operation my command line interface clearly shows its unable to parse the command as a line feed ^M is adding up at end of each line.
I thought sed to be the best way to go about it.I tried:
sed -e 's/^M/d' myfile.txt > myfile1.txt
mv myfile1.txt myfile.txt
It didn't work. I also tried this and it didn't work:
sed -e 's/^M//g' myfile.txt > myfile1.txt
mv myfile1.txt myfile.txt
Then I thought may be sed is taking it as a M character in the beginning of line, and hence no result. So I tried:
sed -e 's/\^M//g' myfile.txt > myfile1.txt
mv myfile1.txt myfile.txt
But no change. Is there a basic mistake I am doing ? Kindly advise as I am bad at sed.
I found a resolution though which was to open the file in vi editor and in command mode execute this:
:set fileformat=unix
:w
But I want it in sed as well.
^M is not literally ^M. Replace ^M with \r. You can use the same representation for tr; these two commands both remove carriage returns:
tr -d '\r' < input.txt > output.txt
sed -e 's/\r//g' input.txt > output.txt
sed -e 's/^M/d' myfile.txt
Has the following meaning [the same for /\^M/ ]: If the first letter of the line is M, then remove the line, else print it and pass to next.. And you have to insert 2 separators /old/new/ in s[earch command].
This may help you.
Late, but here for posterity: sed Delete / Remove ^M Carriage Return (Line Feed / CRLF) on Linux or Unix
The gist, which answers the above question: to get ^M type CTRL+V followed by CTRL+M i.e. don’t just type the carat symbol and a capital M. It will not work

Replace whole line containing a string using Sed

I have a text file which has a particular line something like
sometext sometext sometext TEXT_TO_BE_REPLACED sometext sometext sometext
I need to replace the whole line above with
This line is removed by the admin.
The search keyword is TEXT_TO_BE_REPLACED
I need to write a shell script for this. How can I achieve this using sed?
You can use the change command to replace the entire line, and the -i flag to make the changes in-place. For example, using GNU sed:
sed -i '/TEXT_TO_BE_REPLACED/c\This line is removed by the admin.' /tmp/foo
You need to use wildcards (.*) before and after to replace the whole line:
sed 's/.*TEXT_TO_BE_REPLACED.*/This line is removed by the admin./'
The Answer above:
sed -i '/TEXT_TO_BE_REPLACED/c\This line is removed by the admin.' /tmp/foo
Works fine if the replacement string/line is not a variable.
The issue is that on Redhat 5 the \ after the c escapes the $. A double \\ did not work either (at least on Redhat 5).
Through hit and trial, I discovered that the \ after the c is redundant if your replacement string/line is only a single line. So I did not use \ after the c, used a variable as a single replacement line and it was joy.
The code would look something like:
sed -i "/TEXT_TO_BE_REPLACED/c $REPLACEMENT_TEXT_STRING" /tmp/foo
Note the use of double quotes instead of single quotes.
The accepted answer did not work for me for several reasons:
my version of sed does not like -i with a zero length extension
the syntax of the c\ command is weird and I couldn't get it to work
I didn't realize some of my issues are coming from unescaped slashes
So here is the solution I came up with which I think should work for most cases:
function escape_slashes {
sed 's/\//\\\//g'
}
function change_line {
local OLD_LINE_PATTERN=$1; shift
local NEW_LINE=$1; shift
local FILE=$1
local NEW=$(echo "${NEW_LINE}" | escape_slashes)
# FIX: No space after the option i.
sed -i.bak '/'"${OLD_LINE_PATTERN}"'/s/.*/'"${NEW}"'/' "${FILE}"
mv "${FILE}.bak" /tmp/
}
So the sample usage to fix the problem posed:
change_line "TEXT_TO_BE_REPLACED" "This line is removed by the admin." yourFile
All of the answers provided so far assume that you know something about the text to be replaced which makes sense, since that's what the OP asked. I'm providing an answer that assumes you know nothing about the text to be replaced and that there may be a separate line in the file with the same or similar content that you do not want to be replaced. Furthermore, I'm assuming you know the line number of the line to be replaced.
The following examples demonstrate the removing or changing of text by specific line numbers:
# replace line 17 with some replacement text and make changes in file (-i switch)
# the "-i" switch indicates that we want to change the file. Leave it out if you'd
# just like to see the potential changes output to the terminal window.
# "17s" indicates that we're searching line 17
# ".*" indicates that we want to change the text of the entire line
# "REPLACEMENT-TEXT" is the new text to put on that line
# "PATH-TO-FILE" tells us what file to operate on
sed -i '17s/.*/REPLACEMENT-TEXT/' PATH-TO-FILE
# replace specific text on line 3
sed -i '3s/TEXT-TO-REPLACE/REPLACEMENT-TEXT/'
for manipulation of config files
i came up with this solution inspired by skensell answer
configLine [searchPattern] [replaceLine] [filePath]
it will:
create the file if not exists
replace the whole line (all lines) where searchPattern matched
add replaceLine on the end of the file if pattern was not found
Function:
function configLine {
local OLD_LINE_PATTERN=$1; shift
local NEW_LINE=$1; shift
local FILE=$1
local NEW=$(echo "${NEW_LINE}" | sed 's/\//\\\//g')
touch "${FILE}"
sed -i '/'"${OLD_LINE_PATTERN}"'/{s/.*/'"${NEW}"'/;h};${x;/./{x;q100};x}' "${FILE}"
if [[ $? -ne 100 ]] && [[ ${NEW_LINE} != '' ]]
then
echo "${NEW_LINE}" >> "${FILE}"
fi
}
the crazy exit status magic comes from https://stackoverflow.com/a/12145797/1262663
In my makefile I use this:
#sed -i '/.*Revision:.*/c\'"`svn info -R main.cpp | awk '/^Rev/'`"'' README.md
PS: DO NOT forget that the -i changes actually the text in the file... so if the pattern you defined as "Revision" will change, you will also change the pattern to replace.
Example output:
Abc-Project written by John Doe
Revision: 1190
So if you set the pattern "Revision: 1190" it's obviously not the same as you defined them as "Revision:" only...
bash-4.1$ new_db_host="DB_HOSTNAME=good replaced with 122.334.567.90"
bash-4.1$
bash-4.1$ sed -i "/DB_HOST/c $new_db_host" test4sed
vim test4sed
'
'
'
DB_HOSTNAME=good replaced with 122.334.567.90
'
it works fine
To do this without relying on any GNUisms such as -i without a parameter or c without a linebreak:
sed '/TEXT_TO_BE_REPLACED/c\
This line is removed by the admin.
' infile > tmpfile && mv tmpfile infile
In this (POSIX compliant) form of the command
c\
text
text can consist of one or multiple lines, and linebreaks that should become part of the replacement have to be escaped:
c\
line1\
line2
s/x/y/
where s/x/y/ is a new sed command after the pattern space has been replaced by the two lines
line1
line2
cat find_replace | while read pattern replacement ; do
sed -i "/${pattern}/c ${replacement}" file
done
find_replace file contains 2 columns, c1 with pattern to match, c2 with replacement, the sed loop replaces each line conatining one of the pattern of variable 1
To replace whole line containing a specified string with the content of that line
Text file:
Row: 0 last_time_contacted=0, display_name=Mozart, _id=100, phonebook_bucket_alt=2
Row: 1 last_time_contacted=0, display_name=Bach, _id=101, phonebook_bucket_alt=2
Single string:
$ sed 's/.* display_name=\([[:alpha:]]\+\).*/\1/'
output:
100
101
Multiple strings delimited by white-space:
$ sed 's/.* display_name=\([[:alpha:]]\+\).* _id=\([[:digit:]]\+\).*/\1 \2/'
output:
Mozart 100
Bach 101
Adjust regex to meet your needs
[:alpha] and [:digit:]
are Character Classes and Bracket Expressions
This worked for me:
sed -i <extension> 's/.*<Line to be replaced>.*/<New line to be added>/'
An example is:
sed -i .bak -e '7s/.*version.*/ version = "4.33.0"/'
-i: The extension for the backup file after the replacement. In this case, it is .bak.
-e: The sed script. In this case, it is '7s/.*version.*/ version = "4.33.0"/'. If you want to use a sed file use the -f flag
s: The line number in the file to be replaced. In this case, it is 7s which means line 7.
Note:
If you want to do a recursive find and replace with sed then you can grep to the beginning of the command:
grep -rl --exclude-dir=<directory-to-exclude> --include=\*<Files to include> "<Line to be replaced>" ./ | sed -i <extension> 's/.*<Line to be replaced>.*/<New line to be added>/'
The question asks for solutions using sed, but if that's not a hard requirement then there is another option which might be a wiser choice.
The accepted answer suggests sed -i and describes it as replacing the file in-place, but -i doesn't really do that and instead does the equivalent of sed pattern file > tmp; mv tmp file, preserving ownership and modes. This is not ideal in many circumstances. In general I do not recommend running sed -i non-interactively as part of an automatic process--it's like setting a bomb with a fuse of an unknown length. Sooner or later it will blow up on someone.
To actually edit a file "in place" and replace a line matching a pattern with some other content you would be well served to use an actual text editor. This is how it's done with ed, the standard text editor.
printf '%s\n' '/TEXT_TO_BE_REPLACED/' d i 'This line is removed by the admin' . w q | \
ed -s /tmp/foo > /dev/null
Note that this only replaces the first matching line, which is what the question implied was wanted. This is a material difference from most of the other answers.
That disadvantage aside, there are some advantages to using ed over sed:
You can replace the match with one or multiple lines without any extra effort.
The replacement text can be arbitrarily complex without needing any escaping to protect it.
Most importantly, the original file is opened, modified, and saved. A copy is not made.
How it works
How it works:
printf will use its first argument as a format string and print each of its other arguments using that format, effectively meaning that each argument to printf becomes a line of output, which is all sent to ed on stdin.
The first line is a regex pattern match which causes ed to move its notion of "the current line" forward to the first line that matches (if there is no match the current line is set to the last line of the file).
The next is the d command which instructs ed to delete the entire current line.
After that is the i command which puts ed into insert mode;
after that all subsequent lines entered are written to the current line (or additional lines if there are any embedded newlines). This means you can expand a variable (e.g. "$foo") containing multiple lines here and it will insert all of them.
Insert mode ends when ed sees a line consisting of .
The w command writes the content of the file to disk, and
the q command quits.
The ed command is given the -s switch, putting it into silent mode so it doesn't echo any information as it runs,
the file to be edited is given as an argument to ed,
and, finally, stdout is thrown away to prevent the line matching the regex from being printed.
Some Unix-like systems may (inappropriately) ship without an ed installed, but may still ship with an ex; if so you can simply use it instead. If have vim but no ex or ed you can use vim -e instead. If you have only standard vi but no ex or ed, complain to your sysadmin.
It is as similar to above one..
sed 's/[A-Za-z0-9]*TEXT_TO_BE_REPLACED.[A-Za-z0-9]*/This line is removed by the admin./'
Below command is working for me. Which is working with variables
sed -i "/\<$E\>/c $D" "$B"
I very often use regex to extract data from files I just used that to replace the literal quote \" with // nothing :-)
cat file.csv | egrep '^\"([0-9]{1,3}\.[0-9]{1,3}\.)' | sed s/\"//g | cut -d, -f1 > list.txt

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