Question

I have a text file as shown below. I need only PDB IDs after the > symbol. How can I do this with awk?

>results for sequence "files/1H8U.pdb" starting "ASPILEGLUGLY"
DIEGREKQQPSRVS
>results for sequence "files/1P6K.pdb" starting "ILEALALYSASP"
IAKDVAKEGSDGATKQRTHPQDSASI

Desired output

>1H8U
DIEGREKQQPSRVS
>1P6K
IAKDVAKEGSDGATKQRTHPQDSASI

Answer 1

I would probably use sed for this, but here’s the awk:

awk '/^>/ { sub (/[^\/]+\//,">", $0); sub (/\..+/, "", $0) }1' file.txt

Here’s the sed:

sed -r '/^>/s%[^/]+/%>%;s%\..+%%' file.txt