use web address parameter to enable/disable default tracks?

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use web address parameter to enable/disable default tracks?

CHAN, KENNETH 1 [AG/7721]

Dear all,

  Is there any way (eg. http link) that can enable and disable the default displaying tracks?

This is a more detail description of my intention:

I have another web page which provide gene searching capability. I would like the user clicks on a searched gene to open gbrowse. When gbrowse opens, I would like to have a specific set of tracks to be enabled by default for a specific type of genes. For example,

-          Type1Gene to trigger Track1, Track2 and Track5 to be displayed by default;

-          Type2Gene to trigger Track3 and Track4 to be displayed by default.

I understand that I can use the web address parameter “?name=[Chromosome]%3A[start]..[end]” to specify which chromosome and the start and end positions of the display. Can I have a similar control for the default tracks? Thanks in advance.

 

Regards,

Kenneth

 

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Re: use web address parameter to enable/disable default tracks?

Keiran Raine
Hi Kenneth,

All you need to do is emulate the url generated when you do File-> Bookmark this.

First set up gbrowse page with the tracks you want in the order you want them displayed, then do the bookmark.  The page will reload with a full URL.  You can then use this as a template for generating your links.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100




On 2 Jun 2010, at 09:59, CHAN, KENNETH 1 [AG/7721] wrote:

Dear all,
  Is there any way (eg. http link) that can enable and disable the default displaying tracks?
This is a more detail description of my intention:
I have another web page which provide gene searching capability. I would like the user clicks on a searched gene to open gbrowse. When gbrowse opens, I would like to have a specific set of tracks to be enabled by default for a specific type of genes. For example,
-          Type1Gene to trigger Track1, Track2 and Track5 to be displayed by default;
-          Type2Gene to trigger Track3 and Track4 to be displayed by default.
I understand that I can use the web address parameter “?name=[Chromosome]%3A[start]..[end]” to specify which chromosome and the start and end positions of the display. Can I have a similar control for the default tracks? Thanks in advance.
 
Regards,
Kenneth
 

This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

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Re: use web address parameter to enable/disable default tracks?

CHAN, KENNETH 1 [AG/7721]

Thanks Keiran. But bookmarking the page didn’t give me the same URL at the time of bookmarking, it seems gbrowse is use cookie to remember what tracks has been enable and disable. By the way, I tried on IE6, Firefox v3, and Chrome, but none of them work. Any idea?

 

Regards,

Kenneth

 

 

 

From: Keiran Raine [mailto:[hidden email]]
Sent: Wednesday, June 02, 2010 5:16 PM
To: CHAN, KENNETH 1 [AG/7721]
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] use web address parameter to enable/disable default tracks?

 

Hi Kenneth,

 

All you need to do is emulate the url generated when you do File-> Bookmark this.

 

First set up gbrowse page with the tracks you want in the order you want them displayed, then do the bookmark.  The page will reload with a full URL.  You can then use this as a template for generating your links.

 

Regards,


Keiran Raine

Senior Computer Biologist

The Cancer Genome Project

Ext: 2100

 



 

 

On 2 Jun 2010, at 09:59, CHAN, KENNETH 1 [AG/7721] wrote:



Dear all,

  Is there any way (eg. http link) that can enable and disable the default displaying tracks?

This is a more detail description of my intention:

I have another web page which provide gene searching capability. I would like the user clicks on a searched gene to open gbrowse. When gbrowse opens, I would like to have a specific set of tracks to be enabled by default for a specific type of genes. For example,

-          Type1Gene to trigger Track1, Track2 and Track5 to be displayed by default;

-          Type2Gene to trigger Track3 and Track4 to be displayed by default.

I understand that I can use the web address parameter “?name=[Chromosome]%3A[start]..[end]” to specify which chromosome and the start and end positions of the display. Can I have a similar control for the default tracks? Thanks in advance.

 

Regards,

Kenneth

 

This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.

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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

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Re: use web address parameter to enable/disable default tracks?

Keiran Raine
I think you misunderstand what I mean by bookmarking, you do within the webpage, not through the browser interface, see attached image.



You should be getting something like this:

Single track:
.../?start=1;stop=48129895;ref=21;width=800;version=100;flip=0;grid=1;id=0d44795b2be551d9267d9131a92c8944;l=pindel_ex_ins

Multiple tracks:
.../?start=1;stop=48129895;ref=21;width=800;version=100;flip=0;grid=1;id=0d44795b2be551d9267d9131a92c8944;l=pindel_ex_ins%1Epindel_ex_del%1Epindel_ex_complex

You can drop the 'id=xxx' bit, the l=xxx section is the list of tracks in the order you want them separated by '%1' (the names are those from the config stanzas).

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100




On 2 Jun 2010, at 10:31, CHAN, KENNETH 1 [AG/7721] wrote:

Thanks Keiran. But bookmarking the page didn’t give me the same URL at the time of bookmarking, it seems gbrowse is use cookie to remember what tracks has been enable and disable. By the way, I tried on IE6, Firefox v3, and Chrome, but none of them work. Any idea?
 
Regards,
Kenneth
 
 
 
From: Keiran Raine [[hidden email]] 
Sent: Wednesday, June 02, 2010 5:16 PM
To: CHAN, KENNETH 1 [AG/7721]
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] use web address parameter to enable/disable default tracks?
 
Hi Kenneth,
 
All you need to do is emulate the url generated when you do File-> Bookmark this.
 
First set up gbrowse page with the tracks you want in the order you want them displayed, then do the bookmark.  The page will reload with a full URL.  You can then use this as a template for generating your links.
 
Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100
 


 
 
On 2 Jun 2010, at 09:59, CHAN, KENNETH 1 [AG/7721] wrote:


Dear all,
  Is there any way (eg. http link) that can enable and disable the default displaying tracks?
This is a more detail description of my intention:
I have another web page which provide gene searching capability. I would like the user clicks on a searched gene to open gbrowse. When gbrowse opens, I would like to have a specific set of tracks to be enabled by default for a specific type of genes. For example,
-          Type1Gene to trigger Track1, Track2 and Track5 to be displayed by default;
-          Type2Gene to trigger Track3 and Track4 to be displayed by default.
I understand that I can use the web address parameter “?name=[Chromosome]%3A[start]..[end]” to specify which chromosome and the start and end positions of the display. Can I have a similar control for the default tracks? Thanks in advance.
 
Regards,
Kenneth
 

This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.

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This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.



-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

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Re: use web address parameter to enable/disable default tracks?

CHAN, KENNETH 1 [AG/7721]

It works. Thanks heaps Keiran!!!

 

Regards,

Kenneth

 

 

 

From: Keiran Raine [mailto:[hidden email]]
Sent: Wednesday, June 02, 2010 5:52 PM
To: CHAN, KENNETH 1 [AG/7721]
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] use web address parameter to enable/disable default tracks?

 

I think you misunderstand what I mean by bookmarking, you do within the webpage, not through the browser interface, see attached image.

 

 

 

You should be getting something like this:

 

Single track:

.../?start=1;stop=48129895;ref=21;width=800;version=100;flip=0;grid=1;id=0d44795b2be551d9267d9131a92c8944;l=pindel_ex_ins

 

Multiple tracks:

.../?start=1;stop=48129895;ref=21;width=800;version=100;flip=0;grid=1;id=0d44795b2be551d9267d9131a92c8944;l=pindel_ex_ins%1Epindel_ex_del%1Epindel_ex_complex

 

You can drop the 'id=xxx' bit, the l=xxx section is the list of tracks in the order you want them separated by '%1' (the names are those from the config stanzas).


Keiran Raine

Senior Computer Biologist

The Cancer Genome Project

Ext: 2100

 

 

 

 

On 2 Jun 2010, at 10:31, CHAN, KENNETH 1 [AG/7721] wrote:



Thanks Keiran. But bookmarking the page didn’t give me the same URL at the time of bookmarking, it seems gbrowse is use cookie to remember what tracks has been enable and disable. By the way, I tried on IE6, Firefox v3, and Chrome, but none of them work. Any idea?

 

Regards,

Kenneth

 

 

 

From: Keiran Raine [[hidden email]] 
Sent: Wednesday, June 02, 2010 5:16 PM
To: CHAN, KENNETH 1 [AG/7721]
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] use web address parameter to enable/disable default tracks?

 

Hi Kenneth,

 

All you need to do is emulate the url generated when you do File-> Bookmark this.

 

First set up gbrowse page with the tracks you want in the order you want them displayed, then do the bookmark.  The page will reload with a full URL.  You can then use this as a template for generating your links.

 

Regards,


Keiran Raine

Senior Computer Biologist

The Cancer Genome Project

Ext: 2100

 




 

 

On 2 Jun 2010, at 09:59, CHAN, KENNETH 1 [AG/7721] wrote:




Dear all,

  Is there any way (eg. http link) that can enable and disable the default displaying tracks?

This is a more detail description of my intention:

I have another web page which provide gene searching capability. I would like the user clicks on a searched gene to open gbrowse. When gbrowse opens, I would like to have a specific set of tracks to be enabled by default for a specific type of genes. For example,

-          Type1Gene to trigger Track1, Track2 and Track5 to be displayed by default;

-          Type2Gene to trigger Track3 and Track4 to be displayed by default.

I understand that I can use the web address parameter “?name=[Chromosome]%3A[start]..[end]” to specify which chromosome and the start and end positions of the display. Can I have a similar control for the default tracks? Thanks in advance.

 

Regards,

Kenneth

 

This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.

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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.

 


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.

All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.


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DAS error

Miquel Ràmia
Hi all,

I've a problem with a DAS track if anybody could help me. My track shows
red and with this error message:

- Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
not implemented by package Bio::Das -


I've created the track using de output of make_das_conf.pl, here the
parts of my .conf file relevant to the DAS track

[...]

[ucscDAS:database]
description   = D. melanogaster Apr. 2006 (BDGP R5/dm3) Genome at UCSC
db_adaptor    = Bio::Das
db_args       = -source http://genome.cse.ucsc.edu/cgi-bin/das
                -dsn    dm3

das mapmaster = http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3

aggregators =  phastConsElements15way{phastConsElements15way}

[...]

[PHASTCONSELEMENTS15WAY]
feature      = phastConsElements15way
bgcolor      = turquoise
das category = 1.Reference annotations
key          = phastConsElements15way
citation     = These are phastConsElements15way features.
database     = ucscDAS

[...]


I'm using the latest Bio::Graphics::Browser2 version (2.08) installed
from CPAN. Bio::Das is up to date too.

thanks

Miquel


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Re: DAS error

Sen, Taner Z [GDCBA]
Miquel,

I believe you are missing "remote feature" under  "[PHASTCONSELEMENTS15WAY]"

something like:
remote feature=http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3 

and on top for the das map master we use
#DAS reference server
das mapmaster = SELF

I don't know if this would be relevant in your case.

Taner

On Jun 2, 2010, at 10:06 AM, Miquel Ràmia wrote:

> Hi all,
>
> I've a problem with a DAS track if anybody could help me. My track shows
> red and with this error message:
>
> - Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
> not implemented by package Bio::Das -
>
>
> I've created the track using de output of make_das_conf.pl, here the
> parts of my .conf file relevant to the DAS track
>
> [...]
>
> [ucscDAS:database]
> description   = D. melanogaster Apr. 2006 (BDGP R5/dm3) Genome at UCSC
> db_adaptor    = Bio::Das
> db_args       = -source http://genome.cse.ucsc.edu/cgi-bin/das
>        -dsn    dm3
>
> das mapmaster = http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3
>
> aggregators =  phastConsElements15way{phastConsElements15way}
>
> [...]
>
> [PHASTCONSELEMENTS15WAY]
> feature      = phastConsElements15way
> bgcolor      = turquoise
> das category = 1.Reference annotations
> key          = phastConsElements15way
> citation     = These are phastConsElements15way features.
> database     = ucscDAS
>
> [...]
>
>
> I'm using the latest Bio::Graphics::Browser2 version (2.08) installed
> from CPAN. Bio::Das is up to date too.
>
> thanks
>
> Miquel
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: (515) 294-5326
Fax: (515) 294-8280
taner@iastate. edu
http://www.public.iastate.edu/~taner/ 




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Re: DAS error

Miquel Ràmia
Thanks Taner,

But didn't work. With your options, the error changed to:

- Track rendering error: Operation "eq": no method found -



On Wed, 2010-06-02 at 10:12 -0500, Sen, Taner Z [GDCBA] wrote:

> Miquel,
>
> I believe you are missing "remote feature" under  "[PHASTCONSELEMENTS15WAY]"
>
> something like:
> remote feature=http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3 
>
> and on top for the das map master we use
> #DAS reference server
> das mapmaster = SELF
>
> I don't know if this would be relevant in your case.
>
> Taner
>
> On Jun 2, 2010, at 10:06 AM, Miquel Ràmia wrote:
>
> > Hi all,
> >
> > I've a problem with a DAS track if anybody could help me. My track shows
> > red and with this error message:
> >
> > - Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
> > not implemented by package Bio::Das -
> >
> >
> > I've created the track using de output of make_das_conf.pl, here the
> > parts of my .conf file relevant to the DAS track
> >
> > [...]
> >
> > [ucscDAS:database]
> > description   = D. melanogaster Apr. 2006 (BDGP R5/dm3) Genome at UCSC
> > db_adaptor    = Bio::Das
> > db_args       = -source http://genome.cse.ucsc.edu/cgi-bin/das
> >        -dsn    dm3
> >
> > das mapmaster = http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3
> >
> > aggregators =  phastConsElements15way{phastConsElements15way}
> >
> > [...]
> >
> > [PHASTCONSELEMENTS15WAY]
> > feature      = phastConsElements15way
> > bgcolor      = turquoise
> > das category = 1.Reference annotations
> > key          = phastConsElements15way
> > citation     = These are phastConsElements15way features.
> > database     = ucscDAS
> >
> > [...]
> >
> >
> > I'm using the latest Bio::Graphics::Browser2 version (2.08) installed
> > from CPAN. Bio::Das is up to date too.
> >
> > thanks
> >
> > Miquel
> >
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-ARS, MaizeGDB
> Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: (515) 294-5326
> Fax: (515) 294-8280
> taner@iastate. edu
> http://www.public.iastate.edu/~taner/ 
>
>
>




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Re: DAS error

Keiran Raine
Hi,

The error you are now seeing is consistent with those that we see for  
DAS tracks which match the latest revision of the specification (i.e.  
successfully validate on the dasregistry).  We have found that only  
tracks created against older versions of DAS work.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100
[hidden email]




On 2 Jun 2010, at 16:43, Miquel Ràmia wrote:

> Thanks Taner,
>
> But didn't work. With your options, the error changed to:
>
> - Track rendering error: Operation "eq": no method found -
>
>
>
> On Wed, 2010-06-02 at 10:12 -0500, Sen, Taner Z [GDCBA] wrote:
>> Miquel,
>>
>> I believe you are missing "remote feature" under  
>> "[PHASTCONSELEMENTS15WAY]"
>>
>> something like:
>> remote feature=http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3
>>
>> and on top for the das map master we use
>> #DAS reference server
>> das mapmaster = SELF
>>
>> I don't know if this would be relevant in your case.
>>
>> Taner
>>
>> On Jun 2, 2010, at 10:06 AM, Miquel Ràmia wrote:
>>
>>> Hi all,
>>>
>>> I've a problem with a DAS track if anybody could help me. My track  
>>> shows
>>> red and with this error message:
>>>
>>> - Track rendering error: Abstract method  
>>> "Bio::DasI::get_seq_stream" is
>>> not implemented by package Bio::Das -
>>>
>>>
>>> I've created the track using de output of make_das_conf.pl, here the
>>> parts of my .conf file relevant to the DAS track
>>>
>>> [...]
>>>
>>> [ucscDAS:database]
>>> description   = D. melanogaster Apr. 2006 (BDGP R5/dm3) Genome at  
>>> UCSC
>>> db_adaptor    = Bio::Das
>>> db_args       = -source http://genome.cse.ucsc.edu/cgi-bin/das
>>>        -dsn    dm3
>>>
>>> das mapmaster = http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3
>>>
>>> aggregators =  phastConsElements15way{phastConsElements15way}
>>>
>>> [...]
>>>
>>> [PHASTCONSELEMENTS15WAY]
>>> feature      = phastConsElements15way
>>> bgcolor      = turquoise
>>> das category = 1.Reference annotations
>>> key          = phastConsElements15way
>>> citation     = These are phastConsElements15way features.
>>> database     = ucscDAS
>>>
>>> [...]
>>>
>>>
>>> I'm using the latest Bio::Graphics::Browser2 version (2.08)  
>>> installed
>>> from CPAN. Bio::Das is up to date too.
>>>
>>> thanks
>>>
>>> Miquel
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>> Taner Z. Sen, Ph.D.
>> Computational Biologist, USDA-ARS, MaizeGDB
>> Collab. Assist. Prof., Dept. of Genetics, Development and Cell  
>> Biology
>> Iowa State University
>> 1025 Crop Genome Informatics Lab
>> Ames, IA 50011
>> Phone: (515) 294-5326
>> Fax: (515) 294-8280
>> taner@iastate. edu
>> http://www.public.iastate.edu/~taner/
>>
>>
>>
>
>
>
>
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Re: DAS error

Lincoln Stein
In reply to this post by Miquel Ràmia
This error is fixed in version 2.09 (will be released this week).

Lincoln

2010/6/2 Miquel Ràmia <[hidden email]>
Thanks Taner,

But didn't work. With your options, the error changed to:

- Track rendering error: Operation "eq": no method found -



On Wed, 2010-06-02 at 10:12 -0500, Sen, Taner Z [GDCBA] wrote:
> Miquel,
>
> I believe you are missing "remote feature" under  "[PHASTCONSELEMENTS15WAY]"
>
> something like:
> remote feature=http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3
>
> and on top for the das map master we use
> #DAS reference server
> das mapmaster = SELF
>
> I don't know if this would be relevant in your case.
>
> Taner
>
> On Jun 2, 2010, at 10:06 AM, Miquel Ràmia wrote:
>
> > Hi all,
> >
> > I've a problem with a DAS track if anybody could help me. My track shows
> > red and with this error message:
> >
> > - Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
> > not implemented by package Bio::Das -
> >
> >
> > I've created the track using de output of make_das_conf.pl, here the
> > parts of my .conf file relevant to the DAS track
> >
> > [...]
> >
> > [ucscDAS:database]
> > description   = D. melanogaster Apr. 2006 (BDGP R5/dm3) Genome at UCSC
> > db_adaptor    = Bio::Das
> > db_args       = -source http://genome.cse.ucsc.edu/cgi-bin/das
> >             -dsn    dm3
> >
> > das mapmaster = http://genome.cse.ucsc.edu:80/cgi-bin/das/dm3
> >
> > aggregators =  phastConsElements15way{phastConsElements15way}
> >
> > [...]
> >
> > [PHASTCONSELEMENTS15WAY]
> > feature      = phastConsElements15way
> > bgcolor      = turquoise
> > das category = 1.Reference annotations
> > key          = phastConsElements15way
> > citation     = These are phastConsElements15way features.
> > database     = ucscDAS
> >
> > [...]
> >
> >
> > I'm using the latest Bio::Graphics::Browser2 version (2.08) installed
> > from CPAN. Bio::Das is up to date too.
> >
> > thanks
> >
> > Miquel
> >
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-ARS, MaizeGDB
> Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: (515) 294-5326
> Fax: (515) 294-8280
> taner@iastate. edu
> http://www.public.iastate.edu/~taner/
>
>
>




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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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