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GFF datasource not viewing properly in Dalliance #30

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi,

I'm trying to setup a GFF datasource with MyDas locally and then trying to view 
it in a Dalliance Browser (which I also have set up locally). 

I've attached the gff file that I'm trying to read from. The problem is
that the exons in the file don't seem to be grouped together as transcripts 
even though the group attribute in the gff file has been utilized.

Other public sources viewed in the Dalliance browser show exons grouped 
together as transcripts with introns. However, my own source just shows the 
individual exons with no grouping behaviour. There's one particular difference 
I've noticed in the XML data returned from the public servers versus my local 
server:

PUBL<FEATURE id="ENST00000344226-2" label="COLEC12">
        <TYPE id="transcript">transcript</TYPE>
        <METHOD id="protein_coding">protein_coding</METHOD>
        <START>311662</START>
        <END>311807</END>
        <SCORE>-</SCORE>
        <ORIENTATION>-</ORIENTATION>
        <PHASE>-</PHASE>
        <NOTE>Collectin-12 (Collectin placenta protein 1)(hCL-P1)(CL-P1)(Nurse cell scavenger receptor 2)(Scavenger receptor with C-type lectin)(Scavenger receptor class A member 4) [Source:UniProtKB/Swiss-Prot;Acc:Q5KU26]</NOTE>
        <GROUP id="ENST00000344226" type="transcript" label="COLEC12">
          <LINK href="http://ncbi36.ensembl.org/Homo_sapiens//Gene/Summary?t=ENST00000344226">GeneView</LINK>
        </GROUP>
        <GROUP id="ENSG00000158270" type="gene" label="COLEC12" />
      </FEATURE>IC SERVER:

LOCAL SERVER(the one i've set up):
<FEATURE id="GFF_feature_1" label="GFF_feature_1">
<TYPE id="exon"/>
<METHOD id="protein_coding">protein_coding</METHOD>
<START>49727</START>
<END>50240</END>
<ORIENTATION>-</ORIENTATION>
</FEATURE>

Any help would be greatly appreciated. I've faced the same problem when I tried 
setting up Dazzle, and that is why I switched to mydas. This is my first time 
working with DAS servers. Please let me know if you need any other information.

Thank you,
Azad Memon

Original issue reported on code.google.com by azad.me...@gmail.com on 21 Jan 2013 at 8:40

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