I am facing problem with sed command to replace a text. The sed command works perfectly fine when the replacement text is a plane text without any special charachter. But my replacement text includes the unix file system path and hence it is not working. I am getting an error as below, some one please help me in this :
$ ./install2
sed: -e expression #1, char 22: unknown option to `s'
sed: -e expression #1, char 16: unknown option to `s'
$ cat install2
#!/bin/bash
CONFIG=./config
TMPFILE=./tmpFile
while read line
do
var=$(echo $line | cut -d'=' -f1)
val=$(echo $line | cut -d'=' -f2)
sed -i "s/$var/${val}/i" $TMPFILE
done < "$CONFIG"
$ cat config
INSTALLATION_ROOT=/opt/install/user-home/products
DOWNLOAD_HIBERNATE=false
CONFIG_ROOT=/opt/configs/cfgMgmt/products
$ cat tmpFile
<entry key="installationRoot">INSTALLATION_ROOT</entry>
<entry key="configDirectoryRoot">CONFIG_ROOT</entry>
Thanks,
Sunny
Try this sed -i "s|$var|${val}|i" $TMPFILE. Use | instead of / to allow path replacement.
The / characters may be uniformly replaced by any other single character within any given s command.
The / character (or whatever other character is used in its stead) can appear in the regexp or replacement only if it is preceded by a \ character.
sed -i "s#\$var#${val}#i" $TMPFILE
Related
I'm trying to do multiple replacements in a gzipped file and have been having trouble.
zcat PteBra.fa.align.gz | sed -e 's#Simple_repeat/Satellite/Y-chromosome#Simple_repeat/Satellite#g' -e sed 's#Unknown/Unknown/Y-chromosome#Unknown/Unknown#g' -e sed 's#DNA/DNA/TcMar#DNA/TcMar#g' -e sed 's#DNA/DNA/Crypton#DNA/Crypton#g' -e sed 's#DNA/DNA/PIF-Harbinger#DNA/PIF-Harbinger#g' -e sed 's#DNA/DNA/CMC-Chapaev-3#DNA/CMC-Chapaev-3#g' -e sed 's#SINE/SINE/RTE#SINE/RTE#g' > PteBra.fa.align.corrected
Note that I'm using # instead of the standard / because of the presence of / in the text I want to replace. Each individual sed works with no problem but stringing them together yields this consistent error:
sed: -e expression #2, char 3: unterminated `s' command
I have looked all over for a solution but finally, to get the work done, just did all the sed's individually. It takes FOREVER, so I'd like to get this option working.
I've been at this for hours and would appreciate some help.
What am I doing wrong?
Thanks.
You don't have to write -e sed each time! -e will do.
zcat PteBra.fa.align.gz | sed -e 's#Simple_repeat/Satellite/Y-chromosome#Simple_repeat/Satellite#g' -e 's#Unknown/Unknown/Y-chromosome#Unknown/Unknown#g' -e 's#DNA/DNA/TcMar#DNA/TcMar#g' -e 's#DNA/DNA/Crypton#DNA/Crypton#g' -e 's#DNA/DNA/PIF-Harbinger#DNA/PIF-Harbinger#g' -e 's#DNA/DNA/CMC-Chapaev-3#DNA/CMC-Chapaev-3#g' -e 's#SINE/SINE/RTE#SINE/RTE#g' > PteBra.fa.align.corrected
or you can use semicolon inside sed string expression itself
zcat PteBra.fa.align.gz | sed -e '
s#Simple_repeat/Satellite/Y-chromosome#Simple_repeat/Satellite#g;
s#Unknown/Unknown/Y-chromosome#Unknown/Unknown#g;
s#DNA/DNA/TcMar#DNA/TcMar#g;
s#DNA/DNA/Crypton#DNA/Crypton#g;
s#DNA/DNA/PIF-Harbinger#DNA/PIF-Harbinger#g;
s#DNA/DNA/CMC-Chapaev-3#DNA/CMC-Chapaev-3#g;
s#SINE/SINE/RTE#SINE/RTE#g
' > PteBra.fa.align.corrected
As you already have a proper answer, this is not yet another answer
but a small suggestion for the actual operation.
I imagine writing the sed command in a line may be a messy job. How about
preparing a look-up table which describes a replacee and a replacer
in a line as a csv format like:
table.txt
Simple_repeat/Satellite/Y-chromosome,Simple_repeat/Satellite
Unknown/Unknown/Y-chromosome,Unknown/Unknown
DNA/DNA/TcMar,DNA/TcMar
DNA/DNA/Crypton,DNA/Crypton
DNA/DNA/PIF-Harbinger,DNA/PIF-Harbinger
DNA/DNA/CMC-Chapaev-3,DNA/CMC-Chapaev-3
SINE/SINE/RTE,SINE/RTE
Then you can execute the following awk script to replace the strings:
zcat PteBra.fa.align.gz | awk -F, '
NR==FNR {repl[$1] = $2; next}
{
for (r in repl) gsub(r, repl[r])
print
}
' table.txt - > PteBra.fa.align.corrected
Hope this helps.
I am trying to use sed in bash script as follows:
#!/bin/bash
for i in `seq 1 10`;
do
j=$(($i-1))
OLD="-option_something something/string1_${j}.txt"
NEW="-option_somehting something/string1_${i}.txt"
sed -e "s/$OLD/$NEW/g" file_to_edit.txt
# sed -e "s/$OLD/$NEW/g" file_to_edit.txt > file_to_edit.txt.tmp && mv file_to_edit.txt.tmp file_to_edit.txt
done
But I keep getting following error:
sed: -e expression #1, char 71: unknown option tos'`
I tried the commented line as well, but it does not work too.
It works fine on command line. I do not know what is the problem in script.
Any suggestions? Thanks.
You have a / in the value of OLD and NEW, which is the same character you're using as the delimiter in your sed expression. So the final expression ends up looking like:
sed -e "s/-option_something something/string1_${j}.txt/-option_somehting something/string1_${i}.txt/g"
Do you see all the / in there? Consider instead:
sed -e "s|$OLD|$NEW|g" file_to_edit.txt
You can use any character as the delimiter for sed's s command.
I'm trying to use SED to extract text from two words, such as "Account" and "Recognized", and I'd like that the searching be case insensitive. So I tried to use the I parameter, but receive this error message:
cat Security.txt | sed -n "/Account/,/Recognized/pI" | sed -e '1d' -e '$d'
sed: -e expression #1, char 24: extra characters after command
Avoid useless use of cat
/pattern/I is how to specify case-insensitive matching in sed
sed -n "/Account/I,/Recognized/Ip" Security.txt | sed -e '1d' -e '$d'
You can use single sed command to achieve the same:
sed -n '/account/I,/recognized/I{/account/I!{/recognized/I!p}}' Security.txt
Or awk
awk 'BEGIN{IGNORECASE=1} /account/{f=1; next} /recognized/{f=0} f' Security.txt
Reference:
How to select lines between two patterns?
Use:
sed -n "/Account/,/Recognized/Ip"
i.e. change the order to: Ip instead of pI
You have useless use of cat where you should've fed the file directly to sed. Below could be a way of doing it.
$ cat file.txt
Some stuff Account sllslsljjs Security.
Another stuff account name and ffss security.
$ sed -nE 's/^.*account[[:blank:]]*(.*)[[:blank:]]*security.*$/\1/pI' file.txt
sllslsljjs
name and ffss
The [[:blank:]]* is greedy and will strip the spaces before and after the required text. The -E option enables the use of extended regular expressions.
I am using shell script. My requirement is to find and replace the string. The string contains "/" char as well. I am getting error sed: -e expression #1, char 18: unterminated `s' command. Can someone tell how should i replace the string which has "/"?
#!/bin/bash
...
search_string="../conf/TestSystem/Inst1.xml"
rep="Inst1/Instrument.xml"
sed -i 's|${line}|${rep}/g' MasterConfiguration.xml
I tried using another sed command but that one also gave error sed: -e expression #1, char 13: unknown option to `s'
sed -e "s/${line}/${rep}/g" MasterConfiguration.xml > tempfile
Whenever you deal with shell-variables you have to get them out of the "sed-string":
For example:
sed -e "s/"${line}"/"${rep}"/g" MasterConfiguration.xml > tempfile
Otherwise sed will treat the chars as-is and search for ${line} literally:
As you see, nothing happens here.
Furthermore, if your variables contain / you need to use another delimiter for sed. I tend to use ~ in such a case, but you're free to use other chars - just be consequent and don't mix them like in your first example-sed-command:
sed 's~'${line}'~'${rep}'/g' //WRONG
sed 's~'${line}'~'${rep}'~g' //RIGHT
Combine both and it will work:
You can try this sed,
sed -i "s#${line}#${rep}#g" MasterConfiguration.xml
Problem:
Instead you have,
sed -i "s|${line}|${rep}/g" MasterConfiguration.xml
It should be,
sed -i "s|${line}|${rep}|g" MasterConfiguration.xml
Syntax:
sed "s|pattern|replacement|g"
First of all i apologise in case this has been answered before but i couldn't solve my problem.
I need to search a pattern and then replace it with a line of text comprising of both text and variable.Btw i am using bash..
say
$var = "stacko.ver/rulz=" **Note: $var contain double quotes & = & a dot and /**
i want to so the follow
1.Search for ;te.xt = Note: The value to be search contain ; & = and a dot
2.Replace it with
textnum=$var
Of course $var should be replaced with its actual value
My attempts
sed -i "s/;te.xt =/textnum=$var/" file
sed -i "s/;te.xt =/textnum="$var"/" file
sed -i "s/";te.xt ="/"textnum=$var"/" file
None of these actually worked , either sed giving me an error or the value of $var not shown in file
Thanks for the help
Regards
Quoting doesn't help since this is a sed issue, not a bash issue. Just pick a sed s-expression delimiter that doesn't appear in your text:
sed -i "s|;te.xt =|textnum=$var|" file
You can pick any delimiter for s that doesn't appear in your input. sed -e 'streetlight' is a perfectly valid sed command.
I can see the error:
$ var="stacko.ver/rulz="
$ data="foo ;te.xt = bar"
$ sed "s/;te.xt =/textnum=$var/" <<< "$data"
sed: -e expression #1, char 31: unknown option to `s'
The problem is that $var contains a slash, so sed's s/// command is breaking. You need to pick a character that does not appear in $var
$ sed "s#;te.xt =#textnum=$var#" <<< "$data"
foo textnum=stacko.ver/rulz= bar
This can be hard -- what if slash and hash are in $var? Using bash, you can use ANSI-C quoting to use a control character that is unlikely to appear in your data, e.g.
$ sed $'s\037;te.xt =\037textnum=$var\037' <<< "$data"
foo textnum=stacko.ver/rulz= bar