Re: [Gusdev-gusdev] Duplicate reference to db_ref_id: LoadPfam

[Terry C. <tw...@cs...>]

Paul, I see what you mean. Thanks for taking
time out to shed light on this.

Happy holidays,

Terry

On  0, Pjm <pj...@sa...> wrote:
> Hi Chetna, Terry,
> 
> I dunno if this has already been answered. Apologies if so.
> 
> The Pfam-A.full file I used has duplicate entries which is quite normal. In 
> this cut down example you can see two database references to the same 
> protein but the numbers following it are different;
> 
> 	# STOCKHOLM 1.0
> 	#=GF ID   Acyl_CoA_thio
> 	.
> 	.
> 	#=GF DR   PDB; 1c8u A; 147; 281;
> 	#=GF DR   PDB; 1c8u B; 147; 281;
> 	#=GF DR   PDB; 1c8u A; 17; 115;
> 	#=GF DR   PDB; 1c8u B; 17; 115;
> 
> The numbers are the co-ords on the protein that match up to PF02551. 
> Because the code tries to create another DoTS.DbRefPfamEntry for both of 
> these entries it gives a warning for each.
> 
> 	Duplicate reference to db_ref_id 1351 from pfam_entry_id 91
> 	Duplicate reference to db_ref_id 1352 from pfam_entry_id 91
> 
> Does this help?
> Paul.
> 
> Chetna Warade wrote:
> >Hello Terry,
> >
> >Thanks for the log. I am looking at it and observed
> >that the pfam_entry_id in your log is a continous
> >number from the log whereas for me its different. 
> >
> >Thanks again,
> >Chetna
> >
> >--- Terry Clark <tw...@cs...> wrote:
> >
> >>Hi, Chetna,
> >>I also experienced numerous duplicate entries in the
> >>pfam load.
> >>I assumed these were problems with Pfam
> >>organization, and not
> >>being a priority to me, I did not track them down;
> >>but I have
> >>a not in my log to do so. I've attached my Pfam load
> >>output
> >>for comparison.
> >>
> >>Terry
> >>
> >>
> >>
> >>On  0, Chetna Warade <wa...@ya...> wrote:
> >>
> >>>Hello Debbie,
> >>>
> >>>I am loading (commit) Pfam data  in GUS from
> >>
> >>scratch.
> >>
> >>>I am getting few duplicate errors e.g.
> >>>
> >>>Duplicate reference to db_ref_id 621 from
> >>>pfam_entry_id 1073
> >>>
> >>>Is this behavior okey? If not do you have any idea
> >>>about  fixes for this.
> >>>
> >>>Thanks in advance,
> >>>Chetna
> >>>
> >
> >
> >
> >
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