[InterMine Dev] /service/regions/sequence
jwcarlson at lbl.gov
Fri Apr 10 02:33:05 BST 2015
While debugging some of our code I noticed that you're using the service
URI /service/regions/sequence to trigger GenomicRegionFastaServlet
instead of the servlet in earlier releases
GenomicRegionSequenceExportServlet. The 'FastaServlet is also triggered
by the url pattern /service/regions/fasta. I was curious why you've
changed this. We're using the GenomicRegionSequenceExportServlet
internally here. If this is going to be a permanent switch, then I'll
probably want to make a new url pattern so that we don't have to worry
about code merging issues in the future.
While we're on the subject, I'd actually like to extend the
GenomicRegionSequenceExportServlet so that we can use it for dynamically
generating gene upstream/downstream flanking sequence. This is easy
enough to code up, but I wanted to discuss possible syntax for the
region specification in case this can be incorporated into your code.
gbrowse takes regions specifications like gene:<gene> and the like. I
was going to GenomicRegionSearchUtil.parseRegion that could take a
sequence feature to find the location. For our needs, we'd want to make
it a little more pathquery-ish and be able to say
Gene.secondaryIdentifier:<name> or something like that.
Next, do you have ideas on how you'd implement the extendedStart and
extendedEnd in the regions specification syntax?
Just wondering if you had thoughts on this.
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