$ cat pm_1076056_in.fasta
>gi|321257144|ref|XP_003193485.1| flap ...
MGIKGLTG
RTIRMVDH
ECK
>gi|321473340|gb|EFX84308.1| hypothetical ...
MGIKGLTQ
TIRMVDNG
CKQ

##</code><code>##

$ cat oneline.pl 
use strict;
use warnings;

while (<>) {
    /^>/ ? ($. > 1 && print "\n") : chomp;
    print;
}

print "\n";

##</code><code>##

$ perl oneline.pl pm_1076056_in.fasta > pm_1076056_out.fasta

##</code><code>##

$ cat pm_1076056_out.fasta
>gi|321257144|ref|XP_003193485.1| flap ...
MGIKGLTGRTIRMVDHECK
>gi|321473340|gb|EFX84308.1| hypothetical ...
MGIKGLTQTIRMVDNGCKQ