I have a text file, and I want extract the string from each line coming after "OS="
input file line
A0A0A9PBI3_ARUDO Uncharacterized protein OS=Arundo donax OX=35708 PE=4 SV=1
K3Y356_SETIT ATP-dependent DNA helicase OS=Setaria italica OX=4555 PE=3 SV=1
Output desired
OS=Arundo donax
OS=Setaria italica
OR
Arundo donax
Setaria italica
Use GNU grep (or compatible) with extended regex:
grep -Eo "OS=\w+ \w+" file
or basic regex (you need to escape +
grep -o "OS=\w\+ \w\+" file
# or
grep -o "OS=\w* \w*" file
To get everything from OS= up to OX= you can use grep with perl-compatible regex (PCRE) (-P option) if available and make lookahead:
grep -Po "OS=.*(?=OX=)" file
#to also leave out "OS="
#use lookbehind
grep -Po "(?<=OS=).*(?=OX=)" file
#or Keep-out \K
grep -Po "OS=\K.*(?=OX=)" file
or use grep including OX= and remove it with sed afterwards:
grep -o "OS=.*\( OX=\)" file | sed 's/ OX=$//'
Output:
OS=Arundo donax
OS=Setaria italica
In Perl, two non-whitespace "words":
$ perl -lne 'print $1 if /OS=(\S+ \S+)/' input
or everything up to OX=:
$ perl -lne 'print $1 if /OS=(.*?) OX=/' input
or everything up to the next something=:
$ perl -lne 'print $1 if /OS=(.*?) (\w+)=/' input
With your sample input, they all give the same output, but the output would be different with e.g. an input like this:
ABC=something here OS=foo bar doo PE=3 OX=1234
A more robust way is to use sed to parse the full value until the word containing the next = is found. That way it will work on any sized value (e.g. if you have a font with one word or three words).
sed 's/.*OS=\([^=]*\).*/\1/;s/ [^ ]*$//'
The first block grabs everything up to OS=, the second block in the capture group (denoted by \(\)'s) matches upto the next = and can be referred to in the replacement as \1. The next substitution rids the last word which is a fragment from the next assignment.
Note: the ^ in []'s is to exclude match the character in this case everything that is not an = sign.
awk '{print $(NF-4), $(NF-3)}' file
OS=Arundo donax
OS=Setaria italica
or
awk -F= '{sub(/OX/,""); print $(NF-3)}' file
Arundo donax
Setaria italica
OS=or do you want all words betweenOS=andOX=?