Hello, I have a fine containing many lines and I want to search for specific lines beginning with ">" and replace the third and final dot "." in the string with an underscore "_"

File looks like:

>LKTS.24.127.1
TACGGGAGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGTCCGCAGGCGGCCCTTCAAGTCTGCTGTTAAAAAGT
>LKTS.24.127.3
TACGAGGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGTCCGTAGGCGTTTCAACAAGTCATTTGTTAAAGACA


I want:

>LKTS.24.127_1
TACGGGAGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGTCCGCAGGCGGCCCTTCAAGTCTGCTGTTAAAAAGT
>LKTS.24.127_3
TACGAGGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGTCCGTAGGCGTTTCAACAAGTCATTTGTTAAAGACA

Oh, yes, that looks feasible. How did you try to solve it? sed is (probably) the right tool to do that. Where did you stuck?

Maybe something like:

sed -i -e 's/</[^.]*$/_/g' file_1 > file_2

but I get the error bad flag in substitute command: '_'

yes, because you have an unprotected / in your sed (or at least you have 4 instead of 3)

Won't the dot need to be escaped as well to search for an actual dot? Otherwise it will mean "any single character" to sed.

Correct.
All-in-all, wayyyy too complicated for the task. Design your regex as you specified the requirement. Address only lines starting with ">", and replace the third "."

1 members found this post helpful.

Many thanks! That worked! Keri