I a file containing the genome ids following NZ_FLAT01000030.1_173 I need to manipulate those ids like this one: NZ_FLAT01000030.1
I tried some but didn't give me the exact thing.
sed 's/_/\t/' output : NZ FLAT01000030.1_173
sed -r 's/_//' output: NZFLAT01000030.1_173
sed -r 's/_//g' output: NZFLAT01000030.1173
How can I do that by using sed command?
Are you trying to remove the undesrscore and the digits following it?
echo 'NZ_FLAT01000030.1_173' | sed -E 's/_[0-9]+//g'
NZ_FLAT01000030.1
$ echo 'NZ_FLAT01000030.1_173' | sed 's/_[^_]*$//'
NZ_FLAT01000030.1
Related
Using SED I would like to transform several hundred lines in a text file from:
Input example:
https://mysite.demo.com/topics/en-gb/3
https://mysite.demo.com/topics/en-gb/436
https://mysite.demo.com/topics/en-gb/9167
into
Output:
https://mysite.demo.com/topics/en-gb/3/pdf/3.pdf
https://mysite.demo.com/topics/en-gb/436/pdf/436.pdf
https://mysite.demo.com/topics/en-gb/9167/pdf/9167.pdf
I was wondering what SED command I would use to do this?
Many thanks
Run: echo "https://mysite.demo.com/topics/en-gb/3" |\
sed "s|\(https:\/\/mysite.demo.com\/topics\/en-gb\)\/\([0-9]\+\)|\1/\2/pdf/\2.pdf|g"
Output:
https://mysite.demo.com/topics/en-gb/3/pdf/3.pdf
Here I use sed "s|||" instead of sed "s///".
As per your sample input and expected output, this sed command would work:
sed -E 's,(.*\/)([0-9]+$),\1\2\/pdf\/\2\.pdf,g' text_file
Output:
https://mysite.demo.com/topics/en-gb/3/pdf/3.pdf
https://mysite.demo.com/topics/en-gb/436/pdf/436.pdf
https://mysite.demo.com/topics/en-gb/9167/pdf/9167.pdf
I have these line:
"CN=Michael George\, Jou,OU=External,OU=User,DC=Company,DC=en"
I would like to extract these:
Michael George\, Jou
I'm trying with sed:
grep -i "CN" file | sed "s/CN=\(.*\),\(.*\)/\1/g"
But I can't have these result. Could you help me with sed command? Thanks
str="CN=Michael George\, Jou,OU=External,OU=User,DC=Company,DC=en"
echo "${str}" | sed 's/.*CN=\([^=]*\),.*/\1/'
Output:
Michael George\, Jou
I want to extract /battle/result from following the txt file
$ cat sample
user_id=1234 /battle/start
I run following the sed command
$ cat sample | sed 's|.*\(/.*\)|\1|g'
/start
But, result is deleting /battle, so I can't extract it as I want.
What is wrong with it?
You can remove all characters up to last space:
$ sed 's/.* //' <<< "user_id=1234 /battle/start"
/battle/start
or use cut:
$ cut -d' ' -f2 <<< "user_id=1234 /battle/start"
/battle/start
Sed tries to do a greedy (maximal) match, therefore .* matches your whole line up to but not including the second /.
Try:
< sample sed 's|.* \(/.*\)|\1|g'
or
< sample sed 's|[^/]*\(/.*\)|\1|g'
In your RE the .* is greedy and swallows the /battle part, you could try to invert the logic and delete everything in front of /:
cat sample | sed 's/[^/]*//'
Here [^/]* matches everthing that is not a / and replaces it with nothing.
echo user_id=1234 /battle/start |grep -oP '\s\K.*'
/battle/start
echo user_id=1234 /battle/start |sed -r 's/(^.*\s)(.*)/\2/g'
/battle/start
Due to the know prob of mocha-lcov-mocha breaking file paths, I need to fix the current output paths that looks like this:
SF:Vis/test-Guid.coffee
SF:Vis/Guid.coffee
SF:Vis/test-Vis-Edge.coffee
SF:Vis/Vis-Edge.coffee
into
SF:test/Vis/test-Guid.coffee
SF:src/Vis/Guid.coffee
SF:test/Vis/test-Vis-Edge.coffee
SF:src/Vis/Vis-Edge.coffee
I'm not very good with sed, but I got it to work using:
mocha -R mocha-lcov-reporter _coverage/test --recursive | sed 's,SF:,SF:src/,' | sed s',SF.*test.*,SF:test//&,' | sed s',/SF:,,' | sed s',test/src,test,' | ./node_modules/coveralls/bin/coveralls.js
which is basically doing 4 sed commands in sequence
sed 's,SF:,SF:src/,'
sed s',SF.*test.*,SF:test//&,'
sed s',/SF:,,'
sed s',test/src,test,'
my question is if there is a way to do with this one sed command, or use another osx/linux command line tool
Initially put "src/" after every ":" and then if "test" is found on the line replace "src" with "test":
$ sed 's,:,:src/,;/test/s,src,test,' file
SF:test/Vis/test-Guid.coffee
SF:src/Vis/Guid.coffee
SF:test/Vis/test-Vis-Edge.coffee
SF:src/Vis/Vis-Edge.coffee
You could put all the sed commands in a file, one line per command, and just use "sed -e script". But if you just want it on a single command-line, separate with semicolons. This works for me:
sed 's,SF:,SF:src/,;s,SF.*test.*,SF:test//&,;s,SF:,,;s,test/src/,test,'
sed command
sed '\#test#!{s#SF:Vis/#SF:src/Vis/#g};\#SF:Vis/test#{s#SF:Vis/test#SF:test/Vis/test#g};' my_file
Here is an awk version:
awk -F: '/SF/ {$0=$1FS (/test/?"test/":"src/")$2}1' file
SF:test/Vis/test-Guid.coffee
SF:src/Vis/Guid.coffee
SF:test/Vis/test-Vis-Edge.coffee
SF:src/Vis/Vis-Edge.coffee
How it works:
awk -F: ' # Set field separator to ":"
/SF/{ # Does line start with "SF"?
$0=$1FS (/test/?"test/":"src/")$2 # Recreat String by adding "test" if line contains "test", else "src"
}
1 # Print all lines
' file # read the file
Suppose I have a string like this
<start><a></a><a></a><a></a></start>
I want to replace values inside <start></start> like this
<start><ab></ab><ab></ab><ab></ab><more></more><vale></value></start>
How do I do this using Sed?
Try this :
sed 's#<start>.*</start>#<start><ab></ab><ab></ab><ab></ab></start>#' file
I get this line with gnu sed :
sed -r 's#(<start>)(.*)(</start>)#echo "\1"$(echo "\2"\|sed "s:a>:ab>:g")"\3"#ge'
see example:
kent$ echo "<start><a></a><a></a><a></a><foo></foo><bar></bar></start>"|sed -r 's#(<start>)(.*)(</start>)#echo "\1"$(echo "\2"\|sed "s:a>:ab>:g")"\3"#ge'
<start><ab></ab><ab></ab><ab></ab><foo></foo><bar></bar></start>
note
this will replace the tags between <start>s which ending with a . which worked for your example. but if you have <aaa></aaa>:
you could do: (I break it into lines for better reading)
sed -r 's#(<start>)(.*)(</start>)
#echo "\1"$(echo "\2"\|sed "s:<a>:<ab>:g;s:</a>:</ab>:g")"\3"
#ge'
e.g.
kent$ echo "<start><a></a><a></a><a></a><aaa></aaa><aba></aba></start>" \
|sed -r 's#(<start>)(.*)(</start>)#echo "\1"$(echo "\2"\|sed "s:<a>:<ab>:g;s:</a>:</ab>:g")"\3"#ge'
<start><ab></ab><ab></ab><ab></ab><aaa></aaa><aba></aba></start>
sed 's/(\<\/?)a\>/\1ab\>/g' yourfile, though that would get <a></a> that was outside <start> as well...
grep -rl 'abc' a.txt | xargs sed -i 's/abc/def/g'