Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[Ed R. <ero...@ug...>]

NAFeatureImp is a table you should NEVER write to.  It is
essentially an object master class.

The GUS features you want to write to are all views.  These
include Dots.RNAType, Dots.GeneFeature, Dots.Transcript.

GUS uses sub-classing to create the different kinds of
features you load and store.  These subclasses are accessed
through the views.  These views alias the different generic
string/int/tiny fields in NAFeatureImp to give them real
property names.  All sub_class views of NA_Feature_Imp
inheirit the named attributes of the IMP table.  However, ONLY
the views keep track of which generic fields are mapped to
what properties.  So, only use the views to access this table,
otherwise, you may corrupt your data.

The same goes for NASequenceImp, AAFeatureImp and AASequenceImp.

-ed




---- Original message ----
>Date: Fri, 18 Feb 2005 14:13:29 -0200
>From: Alberto Davila <da...@io...>  
>Subject: Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl  
>To: Steve Fischer <sfi...@pc...>
>Cc: Josef Jurek <ju...@cs...>,
gus...@li..., pol...@gm...
>
>Hi Steve,
>
>Yesterday Poliana presented an internal seminar about GUS
(focused on
>tables used by GBParser and GlimmerM), then some questions
arised, maybe
>you (or someone else) could help:
>
>Why we need several "string" columns in "DoTs.NASequenceImp":
>
>DoTs.NASequenceImp
>string1
>string2
>string3
>string4
>string5
>
>What should be stored in the columns of DoTs.FeatureImp :
>
>DoTs.FeatureImp
>int1        ...  int6   
>tinyint1  ...  tinyint6         
>float1     ...  float6  
>text1   
>string1   ...  string50
>
>Finally, (I think this is for Bindu) does the current version
of the
>"ImportPlasmoDBPrediction" plugin support more than one ORF
predicted by
>GlimmerM ? in other words, GlimmerM usually present several
rows of
>predicted ORFs, each one with a score probability, and there
might be
>more than one ORF predicted... and more than one can be a
valid ORF... 
>
>Thanks, Alberto
>
>On Thu, 2005-02-17 at 15:59 -0500, Steve Fischer wrote:
>> luckily we are already adding that in 3.5
>> 
>> see AnalysisAlgorithm in the 3.5 roadmap: 
>> http://www.gusdb.org/wiki/index.php/Gus3.5RoadMap
>> 
>> steve
>> 
>> Josef Jurek wrote:
>> 
>> >Concerning the DoTS.Similarity table which has been discussed
>> >recently, what we at the Preuss lab are really hurting for
>> >is a way to distinguish different Blast analyses (different
>> >blast parameters) of the same subject and query sequences.
>> >A table as simple as:
>> >
>> >   id                             number(10)
>> >   name                           varchar2(255)
>> >   parameters                     varchar2(255)
>> >
>> >so that one could store something as simple as:
>> >
>> >   'Param Set 001'
>> >   '-p blastx -M BLOSUM50 -G 13 -E 2 -e .01 -W 3'
>> >
>> >and a way to link these entries to the rows of
>> >DoTS.Similarity, perhaps in the way that
>> >DoTS.NASequenceKeyword links rows of DoTS.NASequence
>> >and DoTS.Keyword, would work.  If we were to go ahead and
>> >add the table to the schema, we might want to actually
>> >list the parameters individually with a
>> >comment string, perhaps like:
>> >
>> >
>> >   name                          varchar2(255)
>> >   ...
>> >   expectation_threshold         float(22)
>> >   gap_penalty_existence         number(10)
>> >   gap_penalty_extension         number(10)
>> >   ...
>> >   comment                       varchar2(255)
>> >
>> >Are not other people on the list
>> >missing the ability to distinguish
>> >blast results by parameters?
>> >
>> >Thanks, Josef
>> >
>> >
>> >
>> >Josef Jurek, Ph.D.
>> >
>> >Daphne Preuss Laboratory
>> >Molecular Genetics and Cell Biology
>> >The University of Chicago
>> >ju...@cs...
>> >
>> >voice: (773) 834-3985
>> >fax:   (773) 702-6648
>> >
>> >
>
>
>
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-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883