[Genome] download browser graphics programmatically

[Bob Thurman]

Great, I can get this to work, but I'm still running into a couple of 
problems.

1) I would like to control the width of the display (and hence the 
gif).  The help on " Displaying Your Own Annotations in the Genome 
Browser*" *says "Browser lines allow you to configure such things as the 
genome position that the Genome Browser will initially open to, the 
width of the display, and the configuration of the other annotation 
tracks that are shown (or hidden) in the initial display."  But I don't 
see any attribute name in the "Browser Lines" section that will allow me 
to control the width.

2) My gif seems to be getting cut off at the bottom for all the tracks I 
want to display.  Is there a fixed height for the gif and, if so, is 
there a way to get around this limit?

3) I'd like to display individual subtracks from the ENCODE SangerChip 
tracks (there are over 30).  But the help on Browser Lines says "It is 
not possible to display only a subset of the subtracks at this time."  
True?  Any way around this?

Thanks for your help so far.

Bob Thurman

Hiram Clawson wrote:
> Good Morning Bob:
>
> You can use wget to fetch the browser page and its associated .gif
> graphic.  The resulting html file ends up with an unusual name,
> but the .gif file is there too.  For example:
>
> wget --no-directories --recursive --follow-tags=img --html-extension \
> --convert-links \
> 'http://genome.ucsc.edu/cgi-bin/hgTracks?hgt.customText=http://genome-test.cse.ucsc.edu/~hiram/ctDb/bedWigGtfPsl.txt' 
>
>
> This causes the loading of the custom tracks specified, which also 
> controls which tracks are
> displayed and position, note the browser specifications in the custom 
> track file:
>     http://genome-test.cse.ucsc.edu/~hiram/ctDb/bedWigGtfPsl.txt
>
> The resulting .gif file is named something like: 
> hgt_genome_34c6_9eae80.gif
> The hex ID numbers there will be different each time.
> For this particular example, as a bonus, you also get the ideogram 
> graphic:
>      hgtIdeo_genome_34c6_9eae80.gif
>
> --Hiram
>
> Bob Thurman wrote:
>> Hi,
>>
>> I would like a way to generate from within a program or from a unix 
>> command line, a browser screen shot displaying tracks that I load 
>> myself and download that graphic (as with the "PDF/PS" link at the 
>> top of your page). Is this possible?  Is there a way to do this by 
>> piping output through a wget command or something?
>>
>> Thanks,
>>
>> Bob Thurman
>>
>> Dept. of Genome Sciences
>> University of Washington

-- 
===========================================================
Bob Thurman,  Ph.D.                    Research Scientist
Division of Medical Genetics
Noble Lab
J-205 Health Sciences Building
Box 357720
University of Washington
Seattle, WA 98195-7720                 206-543-8916
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