Remove string between two space characters with sed-CodePudding

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?

CodePudding user response：

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.

CodePudding user response：

You can try this sed

sed 's/\(\.[^\s]*\) .[^\s]* \(.*\)/\1 \2/' input_file

This utilizes grouping to exclude the match between the first and second occurance of a space.

Output

>sp.A9L976 Photosystem II protein D1 organism=Lemna minor taxid=4472 gene=psbA

CodePudding user response：

To edit the header of the fasta file as you specify, use this Perl one-liner:

echo '>sp.A9L976 PSBA_LEMMI Photosystem II protein D1 organism=Lemna minor taxid=4472 gene=psbA' | perl -lpe 's{^(>\S \s )\S \s (.*)}{$1$2}'

Prints:

>sp.A9L976 Photosystem II protein D1 organism=Lemna minor taxid=4472 gene=psbA

To edit the file in place:

perl -i.bak -lpe 's{^(>\S \s )\S \s (.*)}{$1$2}' in_file.fasta

The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-p : Loop over the input one line at a time, assigning it to $_ by default. Add print $_ after each loop iteration.
-l : Strip the input line separator ("\n" on *NIX by default) before executing the code in-line, and append it when printing.
-i.bak : Edit input files in-place (overwrite the input file). Before overwriting, save a backup copy of the original file by appending to its name the extension .bak.

Here,
^ : beginning of the line.
> : literal "greater than" character, which marks the beginning of the header in fasta format specifications.
\S : 1 or more non-whitespace characters.
\s : 1 or more whitespace characters.
.* : any character, 0 or more occurrences.
$1, $2 : 1st and 2nd captured pattern. Capture occurs using parentheses: (...).