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

Hang hangsyin at gmail.com
Sun Jan 20 10:08:59 EST 2008


Hi, Scott,
I tried to change sequence-region line to "4   FlyBase  chromosome_arm  1 
1351857 .  .  .  ID=4;Name=4", it doesn't work. "$!" didn't say anything but
"died at line 12".

So, I went ahead with the Bio::DB::SeqFeature::Store. Here is my code to
load the dmel-all-r5.4.gff(from Flybase) to a test database:
=============================================================
use Bio::DB::SeqFeature::Store;
use Bio::DB::SeqFeature::Store::GFF3Loader;
my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
                                         -dsn     => 'dbi:mysql:test',
                                         -user    => 'root',
                                         -pass    => 'XXXXX',
                                         -write   =>  1 );
my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store    => $db,
                                                         -verbose  => 1);
$loader->load(./'dmel-all-r5.4.gff');
=============================================================
I got bunch of errors like this:
"DBD::mysql::execute failed: Table 'test.locationlist' doesn't exist at
C:\Biology\perl\site\lib\Bio\DB\SeqFeature\Store\DBI\mysql.pm line 1316".
The line 1316 in mysql.pm looks like this: $sth->execute($name) or die
$sth->errstr;
I checked the database test after failed loading. There is only one table
created, which call 'meta'. I also tried 'grant all on test to
XXX at localhost' and used that -user and -pass to load gff, it didn't work
either.

Jon


Scott Cain-3 wrote:
> 
> Hi Jon,
> 
> Well, seeing the error message would be helpful, but my first guess
> without is that there are a few things you can try:
> 
>   * removing the "sequence-region" line from the GFF file, adding a line
> like this:
> 
>   4   FlyBase  chromosome_arm  1  1351857 .  .  .  ID=4;Name=4
> 
> and then reloading the database.
> 
>   * Or, you may want to consider using Bio::DB::SeqFeature::Store, since
> Bio::DB::GFF3 doesn't always behave correctly with complex GFF3 (that
> is, with three levels of features (like gene, mRNA and CDS)).
> 
> Scott
> 
> On Sat, 2008-01-19 at 19:49 -0800, Hang wrote:
>> Hi, Scott,
>> 
>> After adding die $!, I know something is wrong at line:
>> "my $segment = $db->segment(-name => '4', -start => 20000, -end =>
>> 25000);"
>> 
>> my gff file is like this:
>> ##gff-version 3
>> ##sequence-region 4 1 1351857
>> 4	FlyBase	transposable_element	2	611	.	+	.
>> ID=FBti0062890;Name=ninja-Dsim-like{}4829;Dbxref=FlyBase_Annotation_IDs:TE62890;derived_cyto_location=-;
>> 4	repeatmasker_dummy	match	2	347	.	+	.
>> ID=:1395923_repeatmasker_dummy;Name=1%2C347-AE003845.4-dummy-RepeatMasker;
>> 4	repeatmasker_dummy	match_part	2	347	2367	+	.
>> ID=:5142029_dummy;Name=:5142029;Parent=:1395923_repeatmasker_dummy;target_type=so;Target=D83207
>> 5860 6210 +;
>> ...
>> ...
>> I really got confused. Any further suggestion? Thank you!
>> 
>> Jon
>> 
>> 
>> 
>> 
>> 
>> Scott Cain-3 wrote:
>> > 
>> > Hi Jon,
>> > 
>> > I think it's funny that you have "or die" on the database opening line,
>> > "or die" on the @features line, but you didn't put one on the $segment
>> > line.  Try adding "or die: $!" to the $segment line to see what it
>> says,
>> > also add a 'print $segment' after you create it and before you try to
>> > get the features from it.  
>> > 
>> > Clearly, the problem is that $segment is not defined (that is, nothing
>> > is in it, not that the wrong thing is in it).  The next trick is to
>> find
>> > out why.  My first guess, without looking at the data set, is that the
>> > arm is not really named '4'.
>> > 
>> > Scott
>> > 
>> > On Sat, 2008-01-19 at 10:25 -0800, Hang wrote:
>> >> 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
>> >> 
>> > -- 
>> >
>> ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                        
>> cain at cshl.edu
>> > GMOD Coordinator (http://www.gmod.org/)                    
>> 216-392-3087
>> > Cold Spring Harbor Laboratory
>> > 
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> > 
>> > 
>> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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