Hi there,
just a simple question. Can I call the sequenceserver main page in a way that I can populate the Query Sequence field automatically (e.g. through POST)?
If not is it easy to add? I don’t mind adding a few lines to the search.erb view.
Thank you very much,
Ioannis
Do you want to open SS with a different query sequence each time or
with the same query sequence always?
Where is this query sequence sitting? your computer? on the computer
SS is installed on? some third computer?
-- Priyam
The query is different every time. It resides within a MySQL database and the user selects it from a Gbrowse instance. I have a gbrowse plugin that can start ncbi web blast searches using the current sequence in gbrowse and blast settings different than the defaults. I would like to do the same using SS to run a blast against a local database. Ideally I would also like to pass to SS custom blast settings as well.
Interesting usage.
The simplest solution probably is,
1. Use SS from the git repository (or source download - tar.gz or
zip). No gem install.
$ git clone https://github.com/yannickwurm/sequenceserver.git
$ cd sequenceserver
$ gem install bundler
$ bundle install
Rest should follow from website.
2. Redirect users from GBrowse to foobar.com/blast?qid=sequence_id
(assuming foobar.com/blast hosts your SS installation)
3. In SS,
a. modify this [1] line so,
get '/' do
qid = params[:qid]
seq = `mysql -e "select seq from seqs where seq_id=#{qid}"` # 3
erb :search, :locals => {:sequence => seq, :databases =>
databases.values.group_by(&:type)}
end
b. and modify this [2] line so,
<textarea name="sequence" id="sequence" spellcheck="false"
autofocus="true" placeholder="Paste your sequence(s) here..." >
<%= sequence %>
</textarea>
I hope this makes sense. Drop us a line is there's any confusion. And
we would like to know once you get this working 
If you already have a URL that can be hit to obtain the desired
sequence, given it's id, from MySQL - say going to
foobar.com/sequences?qid=sequence_id shows sequence with id
sequence_id - there's another approach that might be simpler.
[1]: https://github.com/yannickwurm/sequenceserver/blob/master/lib/sequenceserver.rb#L321
[2]: https://github.com/yannickwurm/sequenceserver/blob/master/views/search.erb#L52
[3]: See Ruby's backtick operator and string interpolation syntax
"#{}", if needed.
-- Priyam
I’m interested in this approach. If a script on the server returns a fasta object, like foobar.com/sequences?qid=sequence_id would it be possible to get sequenceserver to accept something like
foobar.com/blast?qid=./sequences.cgi?qid=sequence_id
… and populate query textarea with FASTA returned from sequences.cgi?
Not automatically. You will have to make modifications.
You could curl sequences.cgi with the given qid instead of running a mysql query to get the sequence in the previous example. Or you could use Ruby’s Net::HTTP library.
Alternatively, you could do this client side:
$.get(‘/sequence.cgi’ + window.location.search, function (data) {
$(‘.sequences’).val(data)
})
The code is just to give you an idea - it’s not tested.
Priyam
Hi Priyam,
Thanks fort he prompt reply!
Yes, exactly. In which Ruby script should the example you gave below be implemented?
With kind regards,
Thomas van Gurp
Owner | Bioinformatician
Deena Bioinformatics
+31(317) 702 709
+31(6) 472 421 09
The example in the email/post to which you responded. Here - https://groups.google.com/d/msg/sequenceserver/Nyw7ADODGMo/0LtsnXOEnjAJ
There, instead of running a mysql query try to curl sequences.cgi to get the sequence instead.
Ah. The URLs in that post have grown stale … L120 lib/sequenceserver/routes.rb and L148 views/search.erb are the parts you are interested in.
If this works for you, we can try to refine and put a hook in sequenceserver to pre-load sequences given a url and sequence id.
Priyam
Ok, I will give it a try. Thanks for the pointers. I’ll get back to you as soon as I have it working J
Thomas