Re: [GUSDEV] InsertSequenceFeature Issue in GUS3.5

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

I had to go back and check on this.  Intron is not supported
by the Unflattener the way it is invoked by
InsertSequenceFeatures.  When we invoke the unflattener,
because the exons in CryptoDB's gbfile were implicit, we set
the unflattener attribute use_magic to true.  This creates
explicit representations of the exons implicitly present in
the encoding of our gene locations.

Unfortunately, use_magic also requires that we set the
structure type to "0" GENE->mRNA->exon
                                 ->CDS

To get the introns which are specifically encoded in your GB
file, you will need to set the structure type to 1 when the
unflattener is invoked.  I made a number of changes to the
plugin for some colleagues a while back so they could
dynamically choose whether or not to use magic and which kind
of structure they wanted to load.  These changes were never
checked into the official GUS release because they involved
significant changes to the commandline interface.  I will dig
up these changes and show you where to make the necessary
modifications.

-ed

---- Original message ----
>Date: Tue, 2 May 2006 11:23:55 -0400
>From: "Kumar, Sanjeev" <San...@ng...>  
>Subject: [GUSDEV] InsertSequenceFeature Issue in GUS3.5  
>To: <gus...@li...>
>
>   Hi Group,
>      I am having little problem with
>   InsertSequenceFeature in our environment.
>      It is loading all features from the genBank file
>   except "intron" feature. I tried to look into the
>   code and found that it is all together skipping the
>   "intron" feature from genBank file. Is that the
>   issue with "BioPerl"?
>
>   Did any one face this issue earlier?
>
>   The version of bioperl in our environment is :1.5.0
>   And I am using very first version of GUS3.5. Do we
>   have any subsequent release like GUS3.5.X?
>   And the file I am trying to load is related to
>   MICROSPORIDIA organism (NC_003238.gbf).
>   ------
>   The genBank2gus.xml has entry for the intron like
>   this:
>   <feature name="intron" table="DoTS::IntronFeature"
>   so="intron">
>       <qualifier name="allele" lost="true"/>
>       <qualifier name="citation"/>
>       <qualifier name="cons_splice"/>
>       <qualifier name="evidence"/>
>       <qualifier name="function"/>
>       <qualifier name="gene" specialcase="gene"/>
>       <qualifier name="label"/>
>       <qualifier name="locus_tag" column="source_id"/>
>       <qualifier name="map"/>
>       <qualifier name="note" specialcase="note"/>
>       <qualifier name="number" column="num"/>
>       <qualifier name="old_locus_tag" lost="true"/>
>       <qualifier name="standard_name"/>
>       <qualifier name="usedin"/>
>       <qualifier name="db_xref" specialcase="dbxref"/>
>     </feature>
>
>   And the intron entry in genBank file looks like
>   this:
>   gene            complement(52254..52444)
>                        /db_xref="GeneID:860376"
>                        /locus_tag="ECU09_0395"
>        CDS            
>   join(complement(52254..52409),complement(52442..52444))
>                        /db_xref="GI:19173160"
>                        /db_xref="GeneID:860376"
>                        /locus_tag="ECU09_0395"
>                        /codon_start=1
>                        /protein_id="NP_596963.1"
>                       
>   /translation="MGSRKTALVKTRLMRALKRNREIPAWKRMMKEHKGEYNRARRHW
>                        RSKKLKIY"
>                        /product="60S RIBOSOMAL PROTEIN
>   L39"
>        misc_feature   
>   join(complement(52260..52409),complement(52442..52444))
>                        /db_xref="CDD:11875"
>                        /locus_tag="ECU09_0395"
>                        /note="RPL39; Region: Ribosomal
>   protein L39E
>                        [Translation, ribosomal
>   structure and biogenesis]"
>        intron          complement(52410..52441)
>                        /locus_tag="ECU09_0395"
>                        /note="intron L39"
>
>   Any help will be appreciated.
>
>   Thanks
>   Sanjeev Kumar
>   Northrop Grumman
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883