[DAS] Re: das track on contigview

Tony Cox avc@sanger.ac.uk
Wed, 27 Nov 2002 16:40:24 +0000 (GMT)


On Wed, 27 Nov 2002, Alex Lam wrote:

can you dump your database and ldas config and put it on an web/ftp site
somewhere. We'll can load it up locally and see if we can replicate the problem.

tony


+>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
+>
+>
+>>>Envelope-to: alex@gene.cimr.cam.ac.uk
+>>>Delivery-date: Wed, 27 Nov 2002 16:16:16 +0000
+>>>X-Authentication-Warning: alpha1.ebi.ac.uk: majordom set sender to
+>owner-ensembl-dev@alpha1.ebi.ac.uk using -f
+>>>Date: Wed, 27 Nov 2002 16:13:17 +0000 (GMT)
+>>>From: Tony Cox <avc@sanger.ac.uk>
+>>>X-X-Sender: avc@cbi1a.internal.sanger.ac.uk
+>>>To: Alex Lam <Alex.Lam@cimr.cam.ac.uk>
+>>>cc: ensembl-dev@ebi.ac.uk, "" <das@biodas.org>
+>>>Subject: Re: das track on contigview
+>>>MIME-Version: 1.0
+>>>X-Spam-Status: No, hits=-7.3 required=5.0
+>tests=EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES,SPAM_PHRASE_00_01, USER_AGENT_PINE
+>version=2.41
+>>>X-Spam-Level:
+>>>
+>>>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/
+>

******************************************************
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
******************************************************