[Bioperl-l] Question on SeqFeature_RelationShip

lajus florian.lajus at inria.fr
Wed Jan 11 08:09:44 EST 2012


Therefore, if I look in verbose mode, I can see that in the stack I have 
many :

no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::DB::Persistent::PersistentObjectFactory

Just warning, no errors but...
Any clues?

Thanks by advance,

Florian

Le 11/01/2012 13:43, lajus a écrit :
> I have looked to the Unflattener and  the magic works quite fine.
> Then, the $seq which is given (by side-effect)  by
> $unflattener->unflatten_seq(-seq=>$seq, -use_magic=>1);
> has a good hierarchy for us.
> So I'm asking why can't I store this Bio::Seq in my database? Now 
> there is an explicit parent/child links between the gene and CDS.
> But when I create a persitent object for $seq and if I create it:
>     $adaptor->create_persistent($seq);
>     $pseq->create();
> In my database, the bioentry and subseqFeatures are written but still 
> no relation in the seqFeature_relationship table.
>
> Do you have an explanation?
>
> Florian
>
> Le 10/01/2012 19:45, Fields, Christopher J a écrit :
>> On Jan 10, 2012, at 12:18 PM, Peter Cock wrote:
>>
>>> On Tue, Jan 10, 2012 at 5:06 PM, lajus<florian.lajus at inria.fr>  wrote:
>>>> Hello,
>>>> I am currently working on a refactoring of the Genolevures project
>>>> (http://www.genolevures.org/)
>>>> We are trying to better use bioperl and the bioSQL shema on a 
>>>> postgreSQL
>>>> database.
>>>>
>>>> I have loaded an EMBL file into my BioSQL database (postgres). If I 
>>>> look in
>>>> my database, my bioentry have been added and seqFeatures associated 
>>>> too.
>>>> But it seems that my seqfeature_relationship table is empty.
>>>> I find it strange in so far as there is a relationship between gene 
>>>> and its
>>>> CDS. right?
>>> No, not explicitly. Unlike GFF3 where there can be (and should be)
>>> explicit parent/child links between the gene and CDS, in GenBank
>>> and EMBL feature tables this is implicit only. I don't know if BioPerl
>>> attempts to infer this kind of relationship, and if it did, if that 
>>> would
>>> get record in the BioSQL tables.
>>>
>>> Peter
>> BioPerl does not attempt to infer these by default (too much magic, 
>> and too many potential issues), but one can use something like the 
>> Unflattener, which does have some magic built-in:
>>
>> https://metacpan.org/module/Bio::SeqFeature::Tools::Unflattener
>>
>> chris
>>
>



More information about the Bioperl-l mailing list