[Bioperl-l] Question on SeqFeature_RelationShip
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
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::DB::Persistent::PersistentObjectFactory
Just warning, no errors but...
Thanks by advance,
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:
> In my database, the bioentry and subseqFeatures are written but still
> no relation in the seqFeature_relationship table.
> Do you have an explanation?
> 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:
>>>> I am currently working on a refactoring of the Genolevures project
>>>> We are trying to better use bioperl and the bioSQL shema on a
>>>> 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
>>>> 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
>>> get record in the BioSQL tables.
>> 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:
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