[DAS] Re: das track on contigview
Alex Lam
Alex Lam <Alex.Lam@cimr.cam.ac.uk>
Wed, 27 Nov 2002 16:35:43 +0000 (GMT)
Yes. For the gene I attached in XML, it does have the all 8 exon entries in the
fdata table.
I also did a "ldasdump.pl --png" to draw the gene and it did draw 8 exons.
However, I could only see 7 exons on contigview, and the last 3'exon became
really long.
Any idea of how to debug this?
Cheers,
Alex
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>>Date: Wed, 27 Nov 2002 16:13:17 +0000 (GMT)
>>From: Tony Cox <avc@sanger.ac.uk>
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>>To: Alex Lam <Alex.Lam@cimr.cam.ac.uk>
>>cc: ensembl-dev@ebi.ac.uk, "" <das@biodas.org>
>>Subject: Re: das track on contigview
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>>On Wed, 27 Nov 2002, Alex Lam wrote:
>>
>>Is the data correct in the LDAS SQL tables? (I mean, did the data get loaded
>>into the tables incorrectly or was the original data bad or is ensembl munging
>>it)
>>
>>Tony
>>
>>
>>
>>+>Hi developers,
>>+>I have an LDAS server serving out transcripts data and a DAS track on our
local
>>+>ensembl website (version 8). Transcripts show up correctly except for every
>>+>transcript the first two exons on plus strand or the last 2 exons on minus
>>+>strand rendered as 1 continuous block. So all genes have 1 fewer exon and
look
>>+>like as if they have a very long UTR.... :(
>>+>
>>+>I just wonder if anyone has seen this before and knows where the problem
lies.
>>+>
>>+>I have attached the xml output from LDAS below. (In this case 169202433 to
>>+>169207936 is just one block, instead of 2 boxes with a hat connector) Any
help
>>+>would be greatly appreciated.
>>+>
>>+>Thanks,
>>+>Alex
>>+>
>>+>
>>+><?xml version="1.0" standalone="yes"?>
>>+><!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
>>+><DASGFF>
>>+><GFF version="1.01"
>>+>href="http://tartana/perl/das/dil_transcripts/features?segment=6%3A169200000
%2C1
>>+>69220000">
>>+><SEGMENT id="6" start="169200000" stop="169220000" version="1.0">
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/32"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169207783</START>
>>+> <END>169207936</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/31"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169211105</START>
>>+> <END>169211254</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/30"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169211352</START>
>>+> <END>169211485</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/29"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169213220</START>
>>+> <END>169213303</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/28"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169214185</START>
>>+> <END>169214315</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/27"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169216402</START>
>>+> <END>169216508</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/26"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169219242</START>
>>+> <END>169219402</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/33"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
>>+> <METHOD id="exon">exon</METHOD>
>>+> <START>169202433</START>
>>+> <END>169205788</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+> <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/25"
>>+>label="AL513547.C6.1.3.mRNA">
>>+> <TYPE id="transcript:curated"
>>+>category="transcription">transcript:curated</TYPE>
>>+> <METHOD id="transcript">transcript</METHOD>
>>+> <START>169202433</START>
>>+> <END>169219402</END>
>>+> <SCORE>-</SCORE>
>>+> <ORIENTATION>-</ORIENTATION>
>>+> <PHASE>0</PHASE>
>>+> <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
>>+> </FEATURE>
>>+>
>>+></SEGMENT>
>>+></GFF>
>>+></DASGFF>
>>+>
>>+>----
>>+>Alex C. Lam
>>+>Computer Associate
>>+>JDRF/WT Diabetes and Inflammation Laboratory
>>+>Cambridge Institute for Medical Research
>>+>Wellcome Trust/MRC Building
>>+>University of Cambridge
>>+>Hills Road, Cambridge, CB2 2XY
>>+>Great Britain
>>+>
>>+>Office: 01223 763229
>>+>Web: http://www-gene.cimr.cam.ac.uk/todd/
>>+>
>>
>>******************************************************
>>Tony Cox Email:avc@sanger.ac.uk
>>Sanger Institute WWW:www.sanger.ac.uk
>>Wellcome Trust Genome Campus Webmaster
>>Hinxton Tel: +44 1223 834244
>>Cambs. CB10 1SA Fax: +44 1223 494919
>>******************************************************
>>
----
Alex C. Lam
Computer Associate
JDRF/WT Diabetes and Inflammation Laboratory
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
University of Cambridge
Hills Road, Cambridge, CB2 2XY
Great Britain
Office: 01223 763229
Web: http://www-gene.cimr.cam.ac.uk/todd/