I want to print a match only of particular lines with sed;
sed '1,4 /regextomatch/p':
sed: -e expression #1, char 5: unknown command: `/'
What is a command for print?
I suggest:
sed -n '1,4{/regextomatch/p}' file
You can use quit command:
sed -n '/regex/p;4q' file
I'd rather do this:
head -n 4 filename | grep regextomatch
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"
I have a sql dump with 300mb that gives me an error on specific line.
But that line is in the middle of the file. What is the best approach?
head -n middleLine dump.sql > output?
Or can i output only the line i need?
You could use sed -n -e 123456p your.dump to print line 123456
If the file is long, consider using
sed -n 'X{p;q}' file
Where X is the line number. It will stop reading the file after reaching that line.
If sed is too slow for your taste you may also use
cat $THE_FILE | head -n $DESIRED_LINE | tail -n 1
You can use sed:
sed -n "x p" dump.sql
where x is the line number.
This might work for you:
sed 'X!d;q' file
where X is the line number.
This can also be done with Perl:
perl -wnl -e '$. == 4444444 and print and exit;' FILENAME.sql
4444444 being the line number you wish to print.
You can also try awk like:
awk 'NR==YOUR_LINE_NO{print}' file_name
If you know a phrase on that line I would use grep. If the phrase is "errortext" use:
$ cat dump.sql | grep "errortext"