#!/usr/bin/env perl

use 5.014;
use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        my ($top, $seq) = split /\n/, $_, 2;
        print '>' unless $. == 1;
        say $top;
        say $seq =~ y/\n//dr;
    }
}

__DATA__
> gi|11SB_CUCMA Train|1 21
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGS
EVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAPKLIFV
AQGFGIRGIAIPGCAETYQT
SSSSSSSSSSSSSSSSSSSSS....................
...........................
.................
..........
> gi|1A43_HUMAN Train|1 24
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPG
RGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWSQTDRANLGTLRGYYNQSEDGSHTIQR
MYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKWETAHEAE
SSSSSSSSSSSSSSSSSSSSSSSS.........................................................................................
.............
..........................................

##</code><code>##

> gi|11SB_CUCMA Train|1 21
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGSEVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAPKLIFVAQGFGIRGIAIPGCAETYQTSSSSSSSSSSSSSSSSSSSSS..........................................................................
> gi|1A43_HUMAN Train|1 24
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWSQTDRANLGTLRGYYNQSEDGSHTIQRMYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKWETAHEAESSSSSSSSSSSSSSSSSSSSSSSS................................................................................................................................................

##</code><code>##

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        my ($top, $seq) = split /\n/, $_, 2;
        print '>' unless $. == 1;
        say $top;
        $seq =~ y/\n//d;
        say $seq;
    }
}

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        my ($top, $seq) = split /\n/, $_, 2;
        print '>' unless $. == 1;
        print "$top\n";
        $seq =~ y/\n//d;
        print "$seq\n";
    }
}