[Genome] download browser graphics programmatically

[Bob Thurman]

Thanks, Hiram.  I tried the URL change you suggested for subtracks, but 
that just makes the wget-downloaded html file name too long for my 
operating system.  And if I use the -O option for wget, then the gifs 
get embedded in that output file, in such a way that I can't see how to 
extract them. 

These subtrack select options have to go in the URL?  No way to use them 
in a "browser" line in the custom track file?

Thanks again,

Bob Thurman

Hiram Clawson wrote:
> Good Morning Bob:
>
> To set the width of your gif image, use a pix=N argument in your
> URL, for example: ... hgTracks?pix=1000&hgt.customText= ...
> to set size of 1000.  The maximum allowed width is 5000.
>
> Your later email indicated you found the bottom of your gif image.
>
> At this time we do not have a simple mechanism to set some sub-tracks
> on and some sub-tracks off for a single composite track.  You would have
> to laboriously set each sub-track on or off in your URL, it would be
> a lot of variables.  For example:
> encodeSangerChip=full  - to get any of the "on" sub-tracks in full mode
> then each individual track, is a 1 or 0 for on or off, here is an example
> with only three tracks on:
> encodeSangerChipH4acHeLa_sel=1
> encodeSangerChipH3K4me3HeLa_sel=1
> encodeSangerChipH3acHeLa_sel=1
> encodeSangerChipCTCF_sel=0
> encodeSangerChipH3K27me3_sel=0
> encodeSangerChipH3K36me3_sel=0
> encodeSangerChipH3K4me1HFL1_sel=0
> encodeSangerChipH3K4me1HeLa_sel=0
> encodeSangerChipH3K4me1Molt4_sel=0
> encodeSangerChipH3K4me1Ptr8_sel=0
> encodeSangerChipH3K4me1_sel=0
> encodeSangerChipH3K4me2HFL1_sel=0
> encodeSangerChipH3K4me2HeLa_sel=0
> encodeSangerChipH3K4me2K562_sel=0
> encodeSangerChipH3K4me2Molt4_sel=0
> encodeSangerChipH3K4me2Ptr8_sel=0
> encodeSangerChipH3K4me2_sel=0
> encodeSangerChipH3K4me3HFL1_sel=0
> encodeSangerChipH3K4me3K562_sel=0
> encodeSangerChipH3K4me3Molt4_sel=0
> encodeSangerChipH3K4me3Ptr8_sel=0
> encodeSangerChipH3K4me3_sel=0
> encodeSangerChipH3K79me3_sel=0
> encodeSangerChipH3K9me3_sel=0
> encodeSangerChipH3acHFL1_sel=0
> encodeSangerChipH3acK562_sel=0
> encodeSangerChipH3acMolt4_sel=0
> encodeSangerChipH3ac_sel=0
> encodeSangerChipH4acHFL1_sel=0
> encodeSangerChipH4acK562_sel=0
> encodeSangerChipH4acMolt4_sel=0
> encodeSangerChipH4ac_sel=0
>
> To find these variables for any particular track, set it up as you would
> like to see in the genome browser, then alter your WEB browser URL
> to read cartDump where it says hgTracks
>
> --Hiram
>
> 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
>>
>

-- 
===========================================================
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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