[DAS] Re: das track on contigview
Alex Lam
Alex Lam <Alex.Lam@cimr.cam.ac.uk>
Mon, 2 Dec 2002 10:13:07 +0000 (GMT)
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Thanks Lincoln. I can find bulk_load_gff.pl now.
Not sure why you couldn't reach the ftp site. I'll have to ask our sysadmin.
Maybe it isn't open to all. Anyway, I have attached the das, conf and sql files
as a tar.gz.
Thanks very much for your help.
Alex
>>Envelope-to: alex@gene.cimr.cam.ac.uk
>>Delivery-date: Fri, 29 Nov 2002 19:28:02 +0000
>>X-Authentication-Warning: alpha1.ebi.ac.uk: majordom set sender to
owner-ensembl-dev@alpha1.ebi.ac.uk using -f
>>From: Lincoln Stein <lstein@cshl.org>
>>To: Alex Lam <Alex.Lam@cimr.cam.ac.uk>, avc@sanger.ac.uk
>>Subject: Re: [DAS] Re: das track on contigview
>>Date: Fri, 29 Nov 2002 14:26:39 -0500
>>User-Agent: KMail/1.4.3
>>Cc: ensembl-dev@ebi.ac.uk, das@biodas.org
>>MIME-Version: 1.0
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TAA31872
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tests=IN_REP_TO,NOSPAM_INC,QUOTED_EMAIL_TEXT,REFERENCES,
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>>
>>Hi,
>>
>>I just went to get those files myself and I can't find them.
>>
>>The bulk_load_gff.pl script is part of BioPerl. You have to install it into
>>your path. Look in:
>>
>> bioperl/scripts/Bio-DB-GFF/bulk_load_gff.pl
>>
>>Lincoln
>>
>>On Wednesday 27 November 2002 12:11 pm, Alex Lam wrote:
>>> 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%3A
>>> >>16920
>>>
>>> 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/
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS@biodas.org
>>> http://biodas.org/mailman/listinfo/das
>>
----
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/
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--Litter_of_Pups_669_000--