$ perl -Mstrict -Mwarnings -E '
open my $fastaFH, q{<}, \ <<EOF or die $!;
> Seq 1
CTGTCA
GTCCTC
> Seq 2
GGCTA
> Seq 3
CATGAG
ATTCG
EOF

my $seqCt = 0;

$seqCt += tr{>}{} while <$fastaFH>;

say $seqCt;'
3
$