[Bioperl-l] Question on SeqFeature_RelationShip

Hilmar Lapp hlapp at drycafe.net
Thu Jan 12 12:49:10 EST 2012


Hi Florian,

Thanks for digging this up - this is what I had in memory, but I ran out of time last night in ascertaining that it is indeed still true.

It'd be awesome if you can add the code to SeqFeatureAdaptor to also persist and retrieve sub-features. I think the object-relational mappings are all there already (in BaseDriver.pm). You could use the handling of bioentry-to-bioentry relationships (or term-to-term relationships) as a template for how to implement this.

	-hilmar

On Jan 12, 2012, at 4:23 AM, lajus wrote:

> Ok, I have looked in BioPerl code and it appears that subSeqFeature are not handled yet:
> comment in SeqFeatureAdaptor.pm for store children function (and attach childrenn too):
> "Bio::SeqFeatureI has a location, annotation, and possibly sub-seqfeatures as children. The latter is not implemented yet."
> 
> So it's totally normal, if it doesn't work.
> Have you started to implement this stuff, or should I rewrite another SeqFeatureAdaptor which handle this ?
> 
> Florian
> 
> Le 11/01/2012 16:44, Fields, Christopher J a écrit :
>> Seems like a possible bug with bioperl-db, I believe hierarchal seqfeatures are stored, but it's worth looking into.  Do you have some example data (genbank file you are using, for instance)?
>> 
>> chris
>> 
>> On Jan 11, 2012, at 7:09 AM, lajus wrote:
>> 
>>> 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
>>>>> 
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> 
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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