Re: [Gusdev-gusdev] GI Number

[Thomas O. <ot...@fi...>]

Hi,

instead of doing
touch $PROJECT_HOME/GUS/Model/schema/VERSION
build GUS/Model install -append # in the $PROJECT_HOME directory...
-- important is the touch

you can also just use the programm
generateGusObjects
to just build the pm's (perl-modul) for this view

I wrote a little bash file, attached, that already (chmod 755 generate.sh)
./generate.sh DoTS GeneFeatureJinal

Cheers,
Thomas


Jhaveri wrote:

>They are created automatically when you compile or build gus
>
>On Monday 27 September 2004 12:50 pm, you wrote:
>  
>
>>What about the PERL objects in Model/ ?  Do we need to modify any of those
>>so they will work with the modified views?
>>
>>-Ed
>>
>>    
>>
>>>From: "Deborah F. Pinney" <pi...@pc...>
>>>Date: 2004/09/27 Mon PM 12:28:38 EDT
>>>To: Angel Pizarro <an...@pc...>
>>>CC: Ed Robinson <ed_...@be...>,
>>>        Jinal Jhaveri <jjh...@vb...>,
>>>        gus...@li...
>>>Subject: Re: [Gusdev-gusdev] GI Number
>>>
>>>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=462293
>>>>67
>>>>
>>>>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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>>>>>          
>>>>>
>>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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