[Bioperl-l] BioSeq method errors with BioSQL sequences

[Hilmar Lapp]

Good hit Marc. Barry, the reason you're getting the exception is 
because the method isn't implemented by the seq object (a Bio::Seq). 
Only a Bio::Seq::RichSeq instance will implement it.

	-hilmar

On Thursday, November 11, 2004, at 03:41  PM, Marc Logghe wrote:

> Hi Barry,
> Have you tried setting the seqfactory type to 'Bio::Seq::RichSeq' ?
> Did not check it, but guess Bio::Seq has no division method, a richseq 
> does.
> HTH,
> Marc
>
>> -----Original Message-----
>> From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
>> Sent: Friday, November 12, 2004 12:35 AM
>> To: bioperl
>> Subject: [Bioperl-l] BioSeq method errors with BioSQL sequences
>>
>>
>> I have code that I have used to grab details from a Bio::Seq
>> object like
>> this:
>>
>> my $locus = $seq->display_name;
>> my $length = $seq->length;
>> my $mol_type = $seq->molecule;
>> my $division = $seq->division;
>>
>> This works great when called on Bio::Seq created like this:
>>
>> use Bio::DB::RefSeq;
>> $db = new Bio::DB::RefSeq;
>> $seq = $db->get_Seq_by_id('NM_006732');
>>
>> But I recently switched the to using a local database and getting my
>> sequence objects like this:
>>
>> my $db_adaptor = Bio::DB::BioDB->new(
>>         -database => 'biosql',
>>         -user     => 'postgres',
>>         -dbname   => 'some_db',
>>         -host     => 'localhost',
>>         -driver   => 'Pg',
>>     );
>> my $tmp_seq = Bio::Seq->new(-accession_number => "$NM_006732",
>>                             -namespace        => "$ncbi");
>> my $seqfact = Bio::Seq::SeqFactory->new(-type => "Bio::Seq");
>> my $adp = $db_adaptor->get_object_adaptor($tmp_seq);
>> my $seq = $adp->find_by_unique_key($tmp_seq, -obj_factory =>
>> $seqfact);
>>
>> The new seq object seems to behave very nicely under most
>> circumstances
>> but it will not execute some methods like these:
>>
>> my $mol_type = $seq->molecule;
>> my $division = $seq->division;
>>
>> I get an error like this:
>>
>> Can't locate object method "division" via package "Bio::Seq" at
>> /usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject
>> .pm line
>> 541, <IN> line 1.
>>
>>
>> I tried to track down where the problem occured and found that in
>> AUTOLOAD for Bio/DB/Persistent/PersistentObject.pm on line
>> 534 and error
>> was being thrown.
>>
>> 534:        $self->throw("Can't locate object method \"$meth\" via
>> package ".
>> 535:                     ref($self))
>> 536:            unless $obj && ($obj ne $self);
>>
>> Checking ref $obj and ref $self gives Bio::Seq and
>> Bio::DB::Persistent::Seq respectively.  That seems to me to indicate
>> that the 'unless' above should be satisfied - $obj exist and is not
>> equal to $self therefore don't throw.  Running $seq->display_name
>> generates the same values for $obj and $self, but it works.  Methods
>> molecule and division throw errors.  Any suggestions?
>>
>> Barry
>>
>> --
>>
>> Barry Moore
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT
>>
>>
>>
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>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------