Bookmarklet To Open User Ucsc Genome Browser For Specific Chromosomal Location

Question

[D W]

I've written a bookmarlet to open a user defined web link, in this specific case a specific genomic location in the UCSC genome broswer.

javascript:d=%22%22+(window.getSelection?window.getSelection():document.getSelection?document.getSelection():document.selection.createRange().text);d=d.replace(/%5Cr%5Cn%7C%5Cr%7C%5Cn/g,%22%20,%22);if(!d)d=prompt(%22Enter%20the%20chromosomal%20location%20(ex.%20chr1:213243007-213243247):%22,%20%22%22);if(d!=null)location=%22http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Denilw&hgS_otherUserSessionName=mrkdOvrExpUniqMonometh&position=%22+escape(d).replace(/%20/g,%22+%22);void%200

There are 24 chromosomes in the human genome that can be displayed and I would like to do the following:

1) Parse the chromosome out of the user entered string

Use a regex in java script to parse 1 from chr1:213243007-213243247 or X from chrX:213243007-213243247

2) Alter the form on UCSC based on the user input

There are 4 tracks or data sets to show for each of the 22 chromosomes, 88 in total. These are available for selection in the Custom Tracks section of UCSC genome browser as per the linke chosen above, say, this

HS0356_chr__CHROMOSOME__duplicates_standard_len_triangle
HS0445_dpwg_chr_chr_CHROMOSOME__duplicates_standard_len_triangle
HS1328_chr__CHROMOSOME__duplicates_standard_len_triangle
HS1329_dpwg_chr_chr_CHROMOSOME__duplicates_standard_len_triangle

Then I would like the drop down menus for the above, where CHROMOSOME is defined in part 1 to be changed from Hide to Full so that only the data for the chromosome of interest will be displayed.

Perhaps something like this would be helpful.

[Pierre Lindenbaum]

a drop down menu with a bookmarklet ? I guess it would be easier to to with greasemonkey....

[D W]

greasemonkey solutions are accepted

Answer 1

[D W]

http://stackoverflow.com/questions/3153250/bookmarklet-to-open-user-defined-link-and-make-user-defined-form-drop-down-box-se

Answer 2

[Istvan Albert]

This question seems to be more about javascript programming rather than bioinformatics. You might have better luck rephrasing and posting it to Stackoverflow.

[D W]

I didn't have luck on stackoverflow.