Re: [Gusdev-gusdev] GI Number

[Angel P. <an...@pc...>]

Deborah F. Pinney wrote:

> locus_tag is not in the list of features in the GBParser. It will have 
> to be added with a table(actually view) destination. Which view is 
> appropriate for this feature? What are the attributes (from the 
> Genbank feature table) for this feature? I'll gladly add this and you 
> can test it or you can add it and test and then commit to cvs.
>
Let me clarify. "locus_tag" is not a GenBank feature, it is a feature 
attribute of the GenBank "gene" feature. The feature is belongs to is 
being mapped to DoTS::GeneFeature. Here is the example from the GB 
record for this feature attribute, available here :
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46229367

 gene <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819&view=gbwithparts>            complement(<6844..>9270)
                     /locus_tag="cgd7_10"


Thomas' suggestion of adding the attribute "locus_tag" to the 
GeneFeature view and recompiling the objects will work in this case, but 
be a problem for anyone else trying to capture this feature attribute.

The GBParser has several known problems, this being one of them. Maybe 
we should start up a wiki for it to aid in development and documentation.

Angel


> It should be added  >line 808, following my %featureNameTableMapping = (
>
> If the attributes are correct in the mapped table (match the genbank 
> attributes), this should work. If this table is not in the 
> %classChildList, it should also be added to the appropriate line also.
>
>                                                -Deborah
>
> On Mon, 27 Sep 2004, Ed Robinson wrote:
>
>> So far, down here, I can tell that it is parsing the files for crypto 
>> correctly, but I is giving me the following error:
>>
>>
>> ********GEtting loc below6844
>>
>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       
>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
>>
>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       
>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
>>
>> Do you have any ideas why it is disliking my locus_tags?  I am 
>> running this without the commit on, if it is looking for this again 
>> in the database.
>>
>> Thanks for all the help on this.  I don't want to change anything 
>> that is working, just figure out how to use it.
>>
>> -Ed
>>
>>
>>
>>
>>
>> Ed Robinson
>> 255 Deerfield Rd
>> Bogart, GA 30622
>> (706)425-9181
>> http://www.electedrobinson.com
>>
>> --Learn more about the face of your neighbor, and less about your own.
>>         -Sargent Shriver
>>
>>
>>
>
>
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