[DAS] Re: das track on contigview

Alex Lam Alex Lam <Alex.Lam@cimr.cam.ac.uk>
Wed, 27 Nov 2002 17:11:38 +0000 (GMT)


Hi Tony,
You can get the files here:
ftp://ftp-gene.cimr.cam.ac.uk/incoming/dil_transcripts.sql
ftp://ftp-gene.cimr.cam.ac.uk/incoming/dil_transcripts.conf
ftp://ftp-gene.cimr.cam.ac.uk/incoming/test_annotation.das
ftp://ftp-gene.cimr.cam.ac.uk/incoming/reference.das

Much appreciated. 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/