Re: [GUSDEV] InsertSequenceFeature Issue in GUS3.5

[Steve F. <sfi...@pc...>]

sanjeev-

take a look at the bioperl unflattener.  read the docs there.   we may 
have it configured to ignore introns, as they are implied by exons.  if 
you figure out how to re-configure the unflattener, and, think that ISF 
should support alternative unflattener configurations, we may need to 
add a command line option to ISF specifying how to configure the unflattener

steve

Kumar, Sanjeev wrote:

> 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
>