shorten (subtract) header and remove empty line in fasta file by perl

Question

I have a fasta file like this with headers like this:

>GL13245678
ABCDEDERFSE

>GL123456789
ABDFDRAGDTGEGAGFDAS

>GL1254367890
AFGHSRSGFGSHSFG

I want to change the header to contain only GL and 6 digits and remove the empty line above each header, like this:

>GL132456
ABCDEDERFSE
>GL123456
ABDFDRAGDTGEGAGFDAS
>GL125436
AFGHSRSGFGSHSFG

Can anyone share a perl script for this? Thanks

Answer 1

Remove anything from headers (lines starting with >) after GL and 6 digits:

s/^>GL\d{6}\K.+//

Only print non-empty (whitespace only) lines:

print if /\S/

Putting it all together:

perl -ne 's/^>GL\d{6}\K.+//; print if /\S/' file