...
my @infiles = @ARGV;    

for my $file ( @infiles ) {
    my ($descriptions, $sequences) = ParseFile( $file );
    
    ... # output the data here    
}

...

sub ParseFile {
    my $file = shift;

    my %descriptions = my %sequences = ();
    open (my $fh,  '<', $file)  or die "Cannot open input file $file: $!\n";
    while ( my $line = <$fh> ) {
        chomp $line;
        if ( $line =~ m/^>(\S+)\s(.+)/ ) {
            $descriptions{$1} = $2;
        } else {
             $sequences{$1} = $.;
        }
    }

    return (\%descriptions, \%sequences);
}

...