[DAS] Re: das track on contigview
Alex Lam
Alex Lam <Alex.Lam@cimr.cam.ac.uk>
Mon, 9 Dec 2002 11:25:55 +0000 (GMT)
--Colony_of_Beavers_300_000
Content-Type: TEXT/plain; charset=us-ascii
Content-MD5: DUKLIfxVEr/XlmE20mNViA==
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/
--Colony_of_Beavers_300_000
Content-Type: TEXT/plain; name="test_annotation.old"; charset=us-ascii; x-unix-mode=0644
Content-Description: test_annotation.old
Content-MD5: yQ2+OjHRFB19Smhd2NWjHA==
[annotations]
#class name type subtype ref start stop strand phase score tstart tend
Transcript AL513547.C6.1.3.mRNA transcript curated 6 169202433 169219402 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169219242 169219402 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169216402 169216508 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169214185 169214315 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169213220 169213303 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169211352 169211485 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169211105 169211254 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169207783 169207936 - . . . .
Transcript AL513547.C6.1.3.mRNA exon curated 6 169202433 169205788 - . . . .
Transcript AL078605.C6.1.mRNA transcript curated 6 169811298 169895611 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169811298 169811331 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169821859 169823613 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169827568 169827748 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169834938 169835039 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169852640 169852812 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169862715 169862807 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169892776 169892982 + . . . .
Transcript AL078605.C6.1.mRNA exon curated 6 169895502 169895611 + . . . .
--Colony_of_Beavers_300_000
Content-Type: TEXT/plain; name="test_annotation.das"; charset=us-ascii; x-unix-mode=0644
Content-Description: test_annotation.das
Content-MD5: ld0GM3TXPkM5ZzJvMKNm4w==
[annotations]
#class name type subtype ref start stop strand phase score tstart tend
Gene AL513547.C6.1.3.mRNA exon curated 6 169219242 169219402 - . . . .
Gene AL513547.C6.1.3.mRNA exon curated 6 169216402 169216508 - . . . .
Gene AL513547.C6.1.3.mRNA exon curated 6 169214185 169214315 - . . . .
Gene AL513547.C6.1.3.mRNA exon curated 6 169213220 169213303 - . . . .
Gene AL513547.C6.1.3.mRNA exon curated 6 169211352 169211485 - . . . .
Gene AL513547.C6.1.3.mRNA exon curated 6 169211105 169211254 - . . . .
Gene AL513547.C6.1.3.mRNA exon curated 6 169207783 169207936 - . . . .
Gene AL513547.C6.1.3.mRNA exon curated 6 169202433 169205788 - . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169811298 169811331 + . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169821859 169823613 + . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169827568 169827748 + . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169834938 169835039 + . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169852640 169852812 + . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169862715 169862807 + . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169892776 169892982 + . . . .
Gene AL078605.C6.1.mRNA exon curated 6 169895502 169895611 + . . . .
--Colony_of_Beavers_300_000--