use strict; use warnings; use feature 'say';
use Test::More tests => 1;

# my $filename = 'gff.annotated.gtf';
# open(my $fh, '<:encoding(UTF-8)', $filename)
#    or die "Can't open $filename: $!";
my $fh = \*DATA;

my @transcript_ids;

while ( my $line = <$fh> ) {
    my @columns = split / /, $line;
    if ( $columns[16] =~ /^[uxis]$/ ) {
        push @transcript_ids, $columns[10];
    }
}

is_deeply(
    \@transcript_ids, [qw/ bb cc dd ee /],
    'the right lines were matched'
);

__DATA__
1: 01 02 03 04 05 06 07 08 09 aa 11 12 13 14 15 a
2: 01 02 03 04 05 06 07 08 09 bb 11 12 13 14 15 u
3: 01 02 03 04 05 06 07 08 09 cc 11 12 13 14 15 x
4: 01 02 03 04 05 06 07 08 09 dd 11 12 13 14 15 i
5: 01 02 03 04 05 06 07 08 09 ee 11 12 13 14 15 s
6: 01 02 03 04 05 06 07 08 09 ff 11 12 13 14 15 z