[Bioperl-l] Question on SeqFeature_RelationShip

Fields, Christopher J cjfields at illinois.edu
Tue Jan 10 13:45:22 EST 2012


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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