[Bioperl-l] Question on SeqFeature_RelationShip

lajus florian.lajus at inria.fr
Wed Jan 11 07:43:04 EST 2012


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
>



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