[Bioperl-pipeline] Re: Hmmpfam Output

[Shawn Hoon]

yup definitely not..well modularized...

;)

shawn

On Wed, 29 Jan 2003, Jer-Ming wrote:

> It wouldn't change the Hmmpfam output , which is in Bio::Tools right?
> 
> Jerm
> 
> ----- Original Message -----
> From: "Shawn Hoon" <shawnh at fugu-sg.org>
> To: "Jer-Ming" <giscjm at nus.edu.sg>
> Cc: <fuguteam at fugu-sg.org>; "BioPipe mailing list"
> <bioperl-pipeline at bioperl.org>
> Sent: Wednesday, January 29, 2003 4:40 PM
> Subject: Re: Hmmpfam Output
> 
> 
> > I have added ProteinAnnotation runnable to avoid copy-paste protein
> annotation runnables.
> > The xml is also updated. It has been tested somewhat, I have yet to write
> a file based system test for this though.
> > Let me know if this causes problems for people, before I start removing
> the Protein Runnables..
> >
> >
> > shawn
> >
> > On Wed, 29 Jan 2003, Jer-Ming wrote:
> >
> > > I'm going to wait for Bala to look through it and make sure that I'm
> making
> > > sense..... ;-P.
> > >
> > >
> > > ----- Original Message -----
> > > From: "Shawn Hoon" <shawnh at fugu-sg.org>
> > > To: "Jer-Ming" <giscjm at nus.edu.sg>
> > > Cc: <fuguteam at fugu-sg.org>; "BioPipe mailing list"
> > > <bioperl-pipeline at bioperl.org>
> > > Sent: Wednesday, January 29, 2003 4:26 PM
> > > Subject: Re: Hmmpfam Output
> > >
> > >
> > > > Should be ok. This smells like copy-paste code :)
> > > >
> > > > shawn
> > > >
> > > > On Wed, 29 Jan 2003, Jer-Ming wrote:
> > > >
> > > > > Actually the code in question belongs to Bio::Tools, hmmpfam.
> > > > >
> > > > > I noticed that the Hmmpfam parser in Bio::Tools is creating
> FeaturePairs
> > > > > with the the additional tag
> > > > > $featurepair->add_tag_value("hid",$feat->{primary});
> > > > >
> > > > > The primary feature in the $featurepair already has the hid set in
> > > > > $feature->primary .. I believe.
> > > > >
> > > > > This is perfectly fine, except that when the features are stored
> into
> > > > > BioSQL, I noticed that the hid field gets stored twice. One as a
> > > > > seqfeature_qualifier_value, and one as an ontology_term. I don't
> think
> > > this
> > > > > duplicate data is neccessary....
> > > > >
> > > > > Is it alright to remove the hid tag?
> > > > >
> > > > > Jerm
> > > > >
> > > > >
> > > >
> > > > --
> > > > ********************************
> > > > * Shawn Hoon
> > > > * http://www.fugu-sg.org/~shawnh
> > > > ********************************
> > > >
> > >
> >
> > --
> > ********************************
> > * Shawn Hoon
> > * http://www.fugu-sg.org/~shawnh
> > ********************************
> >
> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************