[Bioperl-l] How to store results of searches of translated DNA in SeqFeature::Store database of the original DNA?

Doug douglas.hoen at gmail.com
Wed Aug 11 16:53:35 EDT 2010


One more note: I did try using PositionProxy but it failed. It doesn't
implement seq_id() and so can't be stored in the DB:

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::SeqFeatureI::seq_id" is not implemented by
package Bio::SeqFeature::PositionProxy.
This is not your fault - author of Bio::SeqFeature::PositionProxy
should be blamed!

...



On Aug 11, 4:38 pm, Doug <douglas.h... at gmail.com> wrote:
> Hi Scott,
>
> Good idea. Would you happen to know of an existing HMMER3 to GFF3
> converter?
>
> Thanks for your advice,
> -- Doug
>
> On Aug 11, 4:16 pm, Scott Cain <sc... at scottcain.net> wrote:
>
>
>
>
>
> > Hi Doug,
>
> > I don't know if any of the things you've thought of would work; I've
> > never tried it.  My inclination would be to express your data in GFF3
> > and use the standard loader.
>
> > Scott
>
> > On Wed, Aug 11, 2010 at 4:11 PM, Doug <douglas.h... at gmail.com> wrote:
> > > One possible answer to my own question: Use
> > > Bio::SeqFeature::PositionProxy's? Would this work?
>
> > > On Aug 11, 3:13 pm, Doug <douglas.h... at gmail.com> wrote:
> > >> Hi,
>
> > >> I am trying to store in a SeqFeature::Store database the results of
> > >> searches of translated DNA. The DB contains the original DNA
> > >> sequences. For instance, I have done HMMER searches of 6-frame
> > >> translations of the sequences stored in the DB. I want to store these
> > >> results "at" their (equivalent) DNA positions, which I can calculate.
> > >> Preferably, I would like to directly store the SeqFeature::Similarity
> > >> objects that I get from parsing these searches. But they are of course
> > >> located on different coordinate systems than the DNA, so I guess I
> > >> can't (or shouldn't) create a SeqFeature (e.g. Generic) at the correct
> > >> DNA position and then store the Similarity's as sub-SeqFeatures.
>
> > >> I could just set the Similarity's position to the (calculated) DNA
> > >> coordinates, or alternately make a new SeqFeature and copy in the
> > >> attributes I want. But is there a more elegant solution?
>
> > >> Thanks,
> > >> -- Doug
> > >> _______________________________________________
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>
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>
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain dot net
> > GMOD Coordinator (http://gmod.org/)                    216-392-3087
> > Ontario Institute for Cancer Research
>
> > _______________________________________________
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> > Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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