#! perl
use strict;
use warnings;

my $fasta =
'>gi1 cds
ATG fun 
>gi2 cds
ATG fun
>gi3 cds
GGG fun';

my %hdrs;
   $hdrs{$1} = $2 while $fasta =~ / > (.+) \s+ cds \s+ (.*) \s+ fun /gx;

print  " A. Header & sequences are:\n";
printf ">%s cds\n%s\n", $_, $hdrs{$_} for sort keys %hdrs;

my %seqs;

while (my ($key, $value) = each %hdrs)
{
    push @{$seqs{$value}}, $key;
}

print  " B. Only sequences are:\n";
printf "$_\n" for sort keys %seqs;

print " C. Non-redundant sequences are:\n";
printf ">%s cds\n%s\n", ( sort @{$seqs{$_}} )[0], $_ for sort keys %seqs;