[Bioperl-pipeline] Re: Hmmpfam Output

[Jer-Ming]

neat.

Bala, correct me if I'm wrong, but the $feature->primary
should not be $hid, but "ProteinFeature" or "PfamDomain" or something like
that.

Do you want to make the changes (I assume it's also for all the other
protein tools) or would you rather I do that?

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 4:51 PM
Subject: Re: Hmmpfam Output


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