[Bioperl-pipeline] Re: Hmmpfam Output

[Jer-Ming]

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
> ********************************
>