[DAS] Re: das track on contigview
Lincoln Stein
lstein@cshl.org
Fri, 13 Dec 2002 19:18:19 -0500
I'm glad you got it fixed. I'm sorry I wasn't much help.
Lincoln
On Monday 09 December 2002 06:25 am, Alex Lam wrote:
> Hi Tony + Lincoln,
> I have solved the problem now. If I use Gene instead of Transcript in my
> das file, it shows up correctly on ensembl contigview. Don't know why this
> is though.
>
> Attached my original and new das files.
>
> Cheers,
> Alex
>
> >>X-Unix-From: lstein@cshl.org Fri Nov 29 19:28:02 2002
> >>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
> >>Content-Transfer-Encoding: 8bit
> >>X-MIME-Autoconverted: from quoted-printable to 8bit by alpha1.ebi.ac.uk
> >> id
>
> TAA31872
>
> >>X-Spam-Status: No, hits=-10.5 required=5.0
>
> tests=IN_REP_TO,NOSPAM_INC,QUOTED_EMAIL_TEXT,REFERENCES,
> SPAM_PHRASE_00_01,USER_AGENT,USER_AGENT_KMAIL version=2.41
>
> >>X-Spam-Level:
> >>
> >>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/
--
Lincoln Stein
lstein@cshl.org