Hello zw, and welcome to the Monastery!

First, there is a right brace (curly bracket) missing, but that’s hard to see because of the way the code is formatted. A little reformatting —

use strict;
use warnings;

my $filename = 'gff.annotated.gtf';
open(my $fh, '<:encoding(UTF-8)', $filename) or die "Can't open $filen
+ame: $!";

my @transcript_id = ();

my @lines = <$fh>;

foreach my $lines (@lines)
{
    my @column= split /\t/, $lines;

    foreach $element (@column)
    {
        if ($element[16] eq '"u"' || '"x"' || '"i"' || '"s"')
        {
            push @transcript_id, $element[10];
        }

}

print @transcript_id;
[download]

— and the missing brace is easily seen.

Second, you have use strict (good!), so $element needs to be declared with my:

foreach my $element (@column)
#       ^^
[download]

Third, $element is a scalar variable, which on each iteration of the loop holds a single element of the @column array. But the expressions $element[16] and $element[10] reference an entirely different variable, an array named @element which you haven’t declared. In the case of $element[16], you probably just want to use $element. In the case of $element[10], I’m not sure what you want to do; maybe you meant $column[10]?

Fourth, Perl syntax requires that you make each comparison separately:

if ($element eq 'u' ||
    $element eq 'x' ||
    $element eq 'i' ||
    $element eq 's')
{
    push @transcript_id, $column[10];
}
[download]

Fifth, note that in the above snippet I have removed the extra quotation marks. Your problem description implies that you want to test for equality with the character u, not with the 3-character string "u" as you have in your code.

Sixth (and finally!), I think the logic of your inner foreach loop is questionable. Do you want to push to @transcript_id on each match in the line, or only once per line if a match is found? If the latter, you need to break out of the loop after the first match:

foreach $element (@column)
{
    if ($element eq 'u' ||
        $element eq 'x' ||
        $element eq 'i' ||
        $element eq 's')
    {
        push @transcript_id, $column[10];
        last;
    }
}
[download]

Hope that helps,

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