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

[Pjm <pj...@sa...>]

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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