Issue
somehow I can't wrap my head around this. I have the following string:
>sp.A9L976 PSBA_LEMMI Photosystem II protein D1 organism=Lemna minor taxid=4472 gene=psbA
I would like to use sed to remove the string between the 1th and 2nd occurrence of a space. Hence, in this case, the PSBA_LEMMI should be removed. The string between the first two spaces does not contain any special characters.
So far I tried the following:
sed 's/\s.*\s/\s/'
But this removes everything unitl the last occurring space string, resulting in:>sp.A9L976 TESTgene=psbA. I thought by leaving out the greedy expression g sed will only match the first occurrence of the string. I also tried:
sed 's/(?<=\s).*(?=\s)//'
But this did not match / remove anything. Can someone help me out here? What am I missing?
Solution
You can use
sed -E 's/\s+\S+\s+/ /'
sed -E 's/[[:space:]]+[^[:space:]]+[[:space:]]+/ /'
The two POSIX ERE patterns are the same, they match one or more whitespaces, one or more non-whitespaces, and one or more whitespaces, just \s and \S pattern can only be used in the GNU sed version.
Note that you cannot use \s as a whitespace char in the replacement part. \s is a regex pattern, and regex is used in the LHS (left-hand side) to search for whitespaces. So, a literal space is required to replace with a space.
Since you can also use an awk solution you may use
awk '{$2=""}1' file
Here, the lines ("records") are split into "fields" with whitespace (it is the default field separator), and the second field ($2) value is cleared with {$2 = ""} and the 1 forces awk to output the result (calling the default print command).
Answered By - Wiktor Stribiżew