[Genome] question about URL construction

Mon Jun 4 14:29:45 PDT 2007

Hello Jing,

	Sorry to hear that you are still having problems constructing a URL to 
use for a custom track.  Let me break down each of your questions and I 
think we can work this out.

Answer to Problem 1.

	The position to which you would like the browser to open when you first 
view your custom track is defined in a 'browser line' in your custom 
track data file.  For example, if you would like your custom track to 
open at the position you suggest, add this to the beginning of your data 
file:

browser position chrX:000000007-000000054

	The "%3A" is the ASCII Hex symbol for ":", it is not necessary for you 
to add that to the data file.

	You do not need to add the positional information to the URL that you 
construct -- the software will use the starting position from your data 
file.  Read more about browser lines here: 
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BROWSER

Answer to Problem 2.

	The secure website on which your data are located does not appear to be 
accessible from outside of Agilent.  When I tried to access it directly, 
my browser timed out.  This could be due to a firewall at Agilent, or 
other privacy measures, or the data file could just be too large for my 
browser to open.  At any rate, my Internet browser gives a "page cannot 
be displayed" error when trying to access your data here:
https://wcosned2.cos.agilent.com/earray/userdata/probedesign/PI1234/output/GenomeTiling_bed

	Your data must be located on a server that is accessible by our servers.

	If a login and password is required to access data loaded through a 
URL, this information can be included in the URL using the format 
protocol://user:password@server.com/somepath. Only Basic Authentication 
is supported for HTTP. Note that passwords included in URLs are not 
protected. If a password contains a non-alphanumeric character, such as 
@, the character must be replaced by the hexidecimal representation for 
that character. For example, in the password mypwd at wk, the @ character 
should be replaced by %40, resulting in the modified password mypwd%40wk.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

jing_gao at agilent.com wrote:
> Hi,
> 
> Thanks for the help on this topic in the past. I'm still having a little problem here with constructing the URL and have the bed file loaded up to your browser properly.
> 
> I'm attaching my test bed file here. When I loads it directly into your browser by going to your web site and do it manually, everything is beautiful. This is the UCSC URL I'm seeing from the browser:
> http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=93311163&Submit=go+to+genome+browser&position=chrX%3A000000007-000000054
> 
> 
> When I load it in using a constructed URL, there are 2 problems. This is my constructed URL:
> http://genome.ucsc.edu/cgi-bin/hgTracks??org=human&position=chrX&hgt.customText=https://wcosned2.cos.agilent.com/earray/userdata/probedesign/PI1234/output/GenomeTiling_bed
> 
> 
> Problems:
> 
> 1. How do I add the position like: position=chrX%3A000000007-000000054
> 
> This gives the preferred resolution, but what is "3A"? How do I get that string for all chromosomes and all organisms?
> 
> 
> 2. Bigger problem, if you click on my URL you may see, on top of the page, there is an error line:
> 
> Unrecognized format line 1 of custom track: https://wcosned2.cos.agilent.com/earray/userdata/probedesign/PI1234/output/GenomeTiling_bed (note: chrom names are case sensitive)
> 
> 
> Why? The same file loads OK within your browser, why not with my URL?
> 
> 
> A million thanks.
> 
> 
> Jing
> 
> 
> 
>  <<GenomeTiling_bed>> 
> 
> Jing Gao MD PhD
> Sr. R&D Engineer/Scientist
> Agilent Technologies
> 5301 Stevens Creek Rd
> Santa Clara, CA 95051
> Tel: (408) 553-2571
> Email: jing_gao at agilent.com
> 
> 
> 
> 
> -----Original Message-----
> From: Donna Karolchik [mailto:donnak at soe.ucsc.edu] 
> Sent: Thursday, May 03, 2007 1:47 PM
> To: Galt Barber
> Cc: jing_gao at agilent.com; Genome
> Subject: Re: [Genome] question about URL construction
> 
> You have to be a bit careful when you use the db parameter -- it 
> depends on what you want from your URL. If you want the URL to 
> always point to that specific assembly version, it's better to use 
> the db name. However, if you want your URL to always point to the 
> latest assembly version for a genome (i.e. automatically use the 
> newer version if an assembly is updated), then you should use the 
> org name.
> 
> -Donna
> 
> ----- Original Message ----- 
> From: "Galt Barber" <galt at soe.ucsc.edu>
> To: "Donna Karolchik" <donnak at soe.ucsc.edu>
> Cc: <genome at soe.ucsc.edu>; <jing_gao at agilent.com>
> Sent: Thursday, May 03, 2007 1:40 PM
> Subject: Re: [Genome] question about URL construction
> 
> 
>> You can usually just specify the db (e.g. hg18) in the URL
>> (URL=http://server/path/...&db=hg18...), and the system
>> will figure out the org automatically.
>>
>> -Galt
>>
>>
>> On Thu, 3 May 2007, Donna Karolchik wrote:
>>
>>> hi Jing,
>>>
>>> To add to what Galt says, if you are using one of the org names
>>> that contains white space (e.g. D. melanogaster), be sure to 
>>> put a
>>> "+" in place of the white space, i.e. D.+melanogaster.
>>>
>>> -Donna
>>> -----------------------------------
>>> Donna Karolchik
>>> UCSC Genome Bioinformatics Group
>>> http://genome.ucsc.edu
>>>
>>>
>>> ----- Original Message -----
>>> From: "Galt Barber" <galt at soe.ucsc.edu>
>>> To: <jing_gao at agilent.com>
>>> Cc: <genome at soe.ucsc.edu>
>>> Sent: Thursday, May 03, 2007 1:31 PM
>>> Subject: Re: [Genome] question about URL construction
>>>
>>>
>>>> Check out name, description, organism, etc. in dbDB in this
>>>> file:
>>>>
>>>> http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql
>>>>
>>>> -Galt
>>>>
>>>>
>>>> On Thu, 3 May 2007 jing_gao at agilent.com wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>>
>>>>>
>>>>> I'm trying to figure out how to construct an URL to share my
>>>>> annotation tracks with others. I'm following your 
>>>>> instruction
>>>>> on
>>>>> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE,
>>>>>
>>>>> Which works well for human. And I could figure out org=mouse
>>>>> and org=rat.
>>>>>
>>>>>
>>>>>
>>>>> But could you tell me the String values I should use for 
>>>>> "org="
>>>>> in the case for the following species:
>>>>>
>>>>>
>>>>>
>>>>> A. thaliana
>>>>>
>>>>> C. elegans
>>>>>
>>>>> D. melanogaster
>>>>>
>>>>> D. rerio
>>>>>
>>>>> G. gallus
>>>>>
>>>>> H. sapiens        human
>>>>>
>>>>> M. musculus     mouse
>>>>>
>>>>> R. norvegicus   rat
>>>>>
>>>>> S. cerevisiae
>>>>>
>>>>> S. pombe
>>>>>
>>>>> X. tropicalis
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Thank you very much.
>>>>>
>>>>>
>>>>>
>>>>> Jing
>>>>>
>>>>> _______________________________________________
>>>>> Genome maillist  -  Genome at soe.ucsc.edu
>>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>>>>
>>>> _______________________________________________
>>>> Genome maillist  -  Genome at soe.ucsc.edu
>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
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