Re: [Gusdev-gusdev] GI Number

[Deborah F. P. <pi...@pc...>]

Angel is correct. locus_tag is a relatively new (new to the GBParser) 
qualifier for existing features, including gene which is already mapped 
to dots.GeneFeature. Therefore, my advise was wrong, it should not be 
added to the mapping list in the perl module. Adding this field to the 
view should fix the problem for "gene" features.

As genbank adds features and qualifiers and since the parser was tailored 
for genbank records, we are going to encounter this problem again. A 
compounding problem is that a qualifier is generally not exclusive to a 
single feature. In this case, locus_id really should be added to many 
views.

                                                   -Debbie

On Mon, 27 Sep 2004, Angel Pizarro wrote:

> 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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>
>