[DAS] Re: das track on contigview
Tony Cox
avc@sanger.ac.uk
Fri, 29 Nov 2002 11:49:53 +0000 (GMT)
On Fri, 29 Nov 2002, Alex Lam wrote:
+>Hi,
+>Just wondering whether you could replicate the problem?
sorry, havn't had time to get to it yet - over the weekend!
Tony
+>
+>Thanks,
+>Alex
+>
+>>>Envelope-to: alex@gene.cimr.cam.ac.uk
+>>>Delivery-date: Wed, 27 Nov 2002 16:43:18 +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 16:40:24 +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:
+>>>
+>>>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%3A16920
+>0000
+>>>+>%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
+>>>******************************************************
+>>>
+>
+>----
+>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
******************************************************