[Bioperl-l] Problem: Can't call method "features" on an undefined value at BIO::DB::GFF.pl

Hang hangsyin at gmail.com
Sat Jan 19 13:25:59 EST 2008


Hi, everyone,

I met this problem when I was running this script to extract features
overlaps with 4:20,000..25,000. It always responds like "Can't call method
"features" on an undefined value at BIO::DB::GFF.pl line XX".
==============================================================
use Bio::DB::GFF;
use Bio::Tools::GFF;
my $db = Bio::DB::GFF->new(-adaptor => 'dbi::mysql',
                                        -dsn =>
'dbi:mysql:dmel_gff:localhost',
                                        -user => 'XXXX',
                                        -pass => 'XXXX') || die "database
open failed";

my $segment = $db->segment(-name => '4', -start => 20000, -end => 25000);
my @features = $segment->features(-types => ['gene', 'exon', 'intron',
'five_prime_UTR', 'three_prime_UTR', 'CDS']) or die "no features";
print(scalar(@features)."\n");

================================================================
I am using activeperl 5.8.8 and bioperl 1.5.2 under Win32. I loaded
dmel_5.4.gff into mysql database by bulk_load_gff.pl without any error.
Other methods failed also. 

Any help will be deeply appreciated!

Best,
Jon

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