Hi,
thanks for your solution. It is very interesting! Can you comment it a bit?
The only minor modification, I would do - keep the header line:

while (<>) {
#    next if /^ID/;
    chomp;
    ($table = fileparse $ARGV) =~ s/\.txt$// unless $table;
    $col_cnt{$table} ||=  tr/|//;
    
    my ($gene, $cols) = split /\s*\|\s*/, $_, 2;
    $data{$gene}{$table} = $cols;
    $table = '' if eof;
}
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