[Genome] download browser graphics programmatically

[Bob Thurman]

Oops, forget about 2) below -- the gifs are capturing everything after all.

Bob Thurman wrote:
> 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
>>>       
>
>   

-- 
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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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