Track rendering error for just for one base

[Asela Dassanayake]

Hello, 

I am getting the "Track rendering error : calling translate without seq argument" error when I load GBrowse.

The gene I have set up has 39474 bases. 

The above error appears when the range is set to 1..39474 in the "Land Mark Region" text box.

The above error disappears as soon as I set the range to 1..39473 in the "Land Mark Region" text box.

Just one base....

I have searched for an answer every where but couldnt find it. I am using GBrowse 2.03.

My translation track definition looks like this...

[Translation]
glyph          = translation
global feature = 1
height         = 40
fgcolor        = purple
start_codons   = 0
stop_codons    = 1
translation    = 3frame
category       = Reference:3-frame translation
key            = 3-frame translation

and there are exactly 39474 bases in the seq.fa file in the database folder.

any help would greatly appreciated.

Thank you.

Asela Dassanayake

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[Lincoln Stein]

This is probably fixed in the current version of GBrowse (2.48), because a number of off-by-one errors have been quashed since last September. Could you check this?

Lincoln

On Sun, Mar 11, 2012 at 9:32 AM, Asela Dassanayake <[hidden email]> wrote:

Hello, 

I am getting the "Track rendering error : calling translate without seq argument" error when I load GBrowse.

The gene I have set up has 39474 bases. 

The above error appears when the range is set to 1..39474 in the "Land Mark Region" text box.

The above error disappears as soon as I set the range to 1..39473 in the "Land Mark Region" text box.

Just one base....

I have searched for an answer every where but couldnt find it. I am using GBrowse 2.03.

My translation track definition looks like this...

[Translation]
glyph          = translation
global feature = 1
height         = 40
fgcolor        = purple
start_codons   = 0
stop_codons    = 1
translation    = 3frame
category       = Reference:3-frame translation
key            = 3-frame translation

and there are exactly 39474 bases in the seq.fa file in the database folder.

any help would greatly appreciated.

Thank you.

Asela Dassanayake

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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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[Asela Dassanayake]

Hi,

We are unable to update the GBrowse version at present due to some other technical issues. Is there a way to rectify this error by some other means.. maybe modifying the code...

Thanks

Regards

Asela Dassanayake

On Tue, Mar 13, 2012 at 5:01 AM, Lincoln Stein <[hidden email]> wrote:

This is probably fixed in the current version of GBrowse (2.48), because a number of off-by-one errors have been quashed since last September. Could you check this?

Lincoln

On Sun, Mar 11, 2012 at 9:32 AM, Asela Dassanayake <[hidden email]> wrote:

Hello, 

I am getting the "Track rendering error : calling translate without seq argument" error when I load GBrowse.

The gene I have set up has 39474 bases. 

The above error appears when the range is set to 1..39474 in the "Land Mark Region" text box.

The above error disappears as soon as I set the range to 1..39473 in the "Land Mark Region" text box.

Just one base....

I have searched for an answer every where but couldnt find it. I am using GBrowse 2.03.

My translation track definition looks like this...

[Translation]
glyph          = translation
global feature = 1
height         = 40
fgcolor        = purple
start_codons   = 0
stop_codons    = 1
translation    = 3frame
category       = Reference:3-frame translation
key            = 3-frame translation

and there are exactly 39474 bases in the seq.fa file in the database folder.

any help would greatly appreciated.

Thank you.

Asela Dassanayake

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is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
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_______________________________________________
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[hidden email]
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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
<a href="tel:416%20673-8514" value="[phone]" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

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[Lincoln Stein]

Hi Asela,

Updating just Bio::Graphics may fix the problem. Otherwise, send me a copy of the error messages that appear in the server error log when the error occurs and I will see if I can provide a patch to you.

Lincoln

On Mon, Mar 19, 2012 at 4:35 PM, Asela Dassanayake <[hidden email]> wrote:

Hi,

We are unable to update the GBrowse version at present due to some other technical issues. Is there a way to rectify this error by some other means.. maybe modifying the code...

Thanks

Regards

Asela Dassanayake

On Tue, Mar 13, 2012 at 5:01 AM, Lincoln Stein <[hidden email]> wrote:

This is probably fixed in the current version of GBrowse (2.48), because a number of off-by-one errors have been quashed since last September. Could you check this?

Lincoln

On Sun, Mar 11, 2012 at 9:32 AM, Asela Dassanayake <[hidden email]> wrote:

Hello, 

I am getting the "Track rendering error : calling translate without seq argument" error when I load GBrowse.

The gene I have set up has 39474 bases. 

The above error appears when the range is set to 1..39474 in the "Land Mark Region" text box.

The above error disappears as soon as I set the range to 1..39473 in the "Land Mark Region" text box.

Just one base....

I have searched for an answer every where but couldnt find it. I am using GBrowse 2.03.

My translation track definition looks like this...

[Translation]
glyph          = translation
global feature = 1
height         = 40
fgcolor        = purple
start_codons   = 0
stop_codons    = 1
translation    = 3frame
category       = Reference:3-frame translation
key            = 3-frame translation

and there are exactly 39474 bases in the seq.fa file in the database folder.

any help would greatly appreciated.

Thank you.

Asela Dassanayake

------------------------------------------------------------------------------
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The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-dev2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="[phone]" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

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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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