sequenceserver 0.7.7 → 0.7.8

data/lib/sequenceserver/customisation.rb

@@ -1,104 +1,60 @@
 module SequenceServer
   module Customisation
+    ## When not commented out, this method is used to take a
+    ## sequence ID, and return a hyperlink that
+    ## replaces the hit in the BLAST output.
+    ##
+    ## Return the hyperlink to link to, or nil
+    ## to not not include a hyperlink.
+    ##
+    ## When this method
+    ## is commented out, the default link is used. The default
+    ## is a link to the full sequence of
+    ## the hit is displayed (if makeblastdb has been run with
+    ## -parse_seqids), or no link at all otherwise.
+    # def construct_custom_sequence_hyperlink(options)
+    #   ## Example:
+    #   ## sequence_id comes in like "psu|MAL13P1.200 | organism=Plasmodium_falciparum_3D7 | product=mitochondrial"
+    #   ## output: "http://apiloc.bio21.unimelb.edu.au/apiloc/gene/MAL13P1.200"
+    #   matches = options[:sequence_id].match(/^\s*psu\|(\S+) /)
+    #   if matches #if the sequence_id conforms to our expectations
+    #     # All is good. Return the hyperlink.
+    #     return "http://apiloc.bio21.unimelb.edu.au/apiloc/gene/#{matches[1]}"
+    #   else
+    #     # Parsing the sequence_id didn't work. Don't include a hyperlink for this
+    #     # sequence_id, but log that there has been a problem.
+    #     settings.log.warn "Unable to parse sequence id `#{options[:sequence_id]}'"
+    #     # Return nil so no hyperlink is generated.
+    #     return nil
+    #   end
+    # end
 
-    # TODO: move this module to another file perhaps
-    module Uniprot
-      require 'yaml'
-      SINV = YAML.load_file('./ext/uniprot/sinv.yml')
-    end
-
-    def default_link(options)
-      case options[:sequence_id]
-      when /^lcl\|([^\s]*)/
-        id = $1
-        (@all_retrievable_ids ||= []) << id
-        "/get_sequence/?id=#{id}&db=#{options[:databases].join(' ')}" # several dbs... separate by ' '
-      end
-    end
-
-    # Hook into SequenceServer's BLAST result formatting process to insert
-    # links to Hymenopterabase Genome Browser, and/or Uniprot page
-    # corresponding to a 'hit'.
-    def construct_custom_sequence_hyperlinking_line(options)
-      line = "><a href='#{url(default_link(options))}'>#{options[:sequence_id]}</a>"
-      case options[:sequence_id]
-      when /^lcl\|(PB.*-RA) /
-        # pbar cds and protein
-        id = "#{$1}:#{options[:hit_coordinates].join('..')}"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/pbarbatus_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|pbar_(scf\d*) /
-        # pbar genomic
-        id = "#{$1}:#{options[:hit_coordinates].join('..')}"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/pbarbatus_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /lcl\|SI2.2.0/ # => sinv
-        sid = options[:sequence_id]
-
-        # construct Hymenopterabase genome browser link
-        bid = sid.match(/(Si_gnF.scaffold\d*)\[(\d*..\d*)\]/)[1..2].join(':')
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/sinvicta_1/?name=#{bid}"
-
-        # construct uniprot link
-        ukey = sid.match(/SI2.2.0_(\d*)/)[1]
-        uid  = Uniprot::SINV["SINV_#{ukey}"]
-        uniprot = "http://www.uniprot.org/uniprot/#{uid}"
-
-        # construct the entire line
-        line << " [<a href='#{browser}'>Genome Browser</a>] [<a href='#{uniprot}'>Uniprot</a>]\n"
-      when /^lcl\|(Si_gnF.scaffold\d*) /
-        # sinv genomic
-        id = "#{$1}:#{options[:hit_coordinates].join('..')}"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/sinvicta_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|(LH\d*-RA) /
-        # lhum cds and protein
-        id = "#{$1}:#{options[:hit_coordinates].join('..')}"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/lhumile_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|(scf\d*) /
-        # lhum genomic
-        id = "#{$1}:#{options[:hit_coordinates].join('..')}"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/lhumile_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|(ACEP_\d*-RA) /
-        # acep cds and protein
-        id = $1.gsub(/EP_000/, '')
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/acephalotes_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|Acep_(scaffold\d*) /
-        # acep genomic
-        id = $1
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/acephalotes_1/?name=#{id}:#{options[:hit_coordinates].join('..')}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|Cflo_(\d*)--/
-        # cflo cds and protein
-        id = "CFLO#{$1}-RA"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/cfloridanus_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|Cflo_gn3.3_((scaffold\d*)|(C\d*)) /
-        # cflo genomic
-        id = "#{$1}:#{options[:hit_coordinates].join('..')}"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/cfloridanus_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|Hsal_(\d*)--/
-        # hsal cds and protein
-        id = "HSAL#{$1}-RA"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/hsaltator_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      when /^lcl\|Hsal_gn3.3_((scaffold\d*)|(C\d*)) /
-        # hsal genomic
-        id = "#{$1}:#{options[:hit_coordinates].join('..')}"
-        browser = "http://genomes.arc.georgetown.edu/cgi-bin/gbrowse/hsaltator_1/?name=#{id}"
-        line << " [<a href='#{browser}'>Genome Browser</a>]\n"
-      else
-        # Parsing the sequence_id didn't work. Don't include a hyperlink for this
-        # sequence_id, but log that there has been a problem.
-        settings.log.warn "Unable to parse sequence id `#{options[:sequence_id]}'"
-        # Return nil so no hyperlink is generated.
-        return nil
-      end
-      line
-    end
+    ## Much like construct_custom_sequence_hyperlink, except
+    ## instead of just a hyperlink being defined, the whole
+    ## line as it appears in the blast results is generated.
+    ##
+    ## This is a therefore more flexible setup than is possible
+    ## with construct_custom_sequence_hyperlink, because doing
+    ## things such as adding two hyperlinks for the one hit
+    ## are possible.
+    ##
+    ## When this method is commented out, the behaviour is that
+    ## the construct_custom_sequence_hyperlink method is used,
+    ## or failing that the default method of that is used.
+    # def construct_custom_sequence_hyperlinking_line(options)
+    #   matches = options[:sequence_id].match(/^\s*psu\|(\S+) /)
+    #   if matches #if the sequence_id conforms to our expectations
+    #     # All is good. Return the hyperlink.
+    #     link1 = "http://apiloc.bio21.unimelb.edu.au/apiloc/gene/#{matches[1]}"
+    #     link2 = "http://google.com/?q=#{matches[1]}"
+    #     return "<a href='#{link1}'>ApiLoc page</a>, <a href='#{link2}'>Google search</a>"
+    #   else
+    #     # Parsing the sequence_id didn't work. Don't include a hyperlink for this
+    #     # sequence_id, but log that there has been a problem.
+    #     settings.log.warn "Unable to parse sequence id `#{options[:sequence_id]}'"
+    #     # Return nil so no hyperlink is generated.
+    #     return nil
+    #   end
+    # end
   end
-end
+end

data/public/js/sequenceserver.js

@@ -147,7 +147,7 @@ $(document).ready(function(){
         $.onedb();
     });
 
-    $('input:submit').click(function(){
+    $('#blast').submit(function(){
         var button = $(this);
 
         //prevent submitting another query while this one is being processed

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.7.7'
+  s.version     = '0.7.8'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'

data/views/search.erb

@@ -1,13 +1,12 @@
 <!DOCTYPE html>
 <html lang="en">
 <head>
-  <title>Fourmidable: BLAST ant genomes, proteomes, and transcriptomes.</title>
+  <title>SequenceServer: Custom BLAST Server</title>
   <meta name="author" content="Anurag Priyam" />
   <meta name="author" content="Ben J. Woodcroft" />
   <meta name="author" content="Yannick Wurm" />
   <meta name="author" content="Cedric Wurm" />
-  <meta name="description" content="BLAST search for ant genome sequences. A simple blast interface to search sequence of recently published ant genome."/>
-  <meta name="keywords" content="ant genomes, blast search, fire ant genome, harvester ant genome, leafcutter ant genome, camponotus genome, harpegnathos genome."/>
+  <meta name="description" content="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
   <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
   <script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
@@ -18,30 +17,16 @@
   <%# without a space after erb's closing tag, a / gets appended to css' path %>
   <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.min.css') %>" />
   <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/custom.css') %>" />
-
-  <script type="text/javascript">
-    var _gaq = _gaq || [];
-    _gaq.push(['_setAccount', 'UA-471841-4']);
-    _gaq.push(['_setDomainName', 'none']);
-    _gaq.push(['_setAllowLinker', true]);
-    _gaq.push(['_trackPageview']);
-
-    (function() {
-      var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
-      ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
-      var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
-    })();
-  </script>
 </head>
 
 <body>
   <div class="container">
     <div class="page">
       <div class="page-header" id="banner">
-        <h1>BLAST Ant Genomes(s)</h1>
+        <h1>BLAST Sequence(s)</h1>
       </div>
 
-      <form method="post" action="<%= uri('/#result') %>">
+      <form method="post" id="blast" action="<%= uri('/#result') %>">
         <div class="row">
           <div class="span12">
             <div class="offset-left sequence">
@@ -231,8 +216,7 @@
       </div>
 
       <div id="underbar">
-        <p><a href="http://www.isb-sib.ch"><img src="http://antgenomes.org/img/sib120x74.png" width="40" height="25" alt="SIBlogo"/></a> Hosted by the Swiss Institute of Bioinformatics. BLAST search by <a href="http://www.sequenceserver.com">SequenceServer</a>.</p>
-        <p>Please cite: <a href="http://www.biomedcentral.com/1471-2164/10/5/abstract">Wurm <em>et al</em> (2009) <strong>Fourmidable: a database for ant genomics.</strong> <em>BMC Genomics</em> 10:5</a> and the appropriate ant genome paper(s).</p>
+        <p>&copy; <a href='http://www.sequenceserver.com'>SequenceServer: BLAST search made easy!</a></p>
       </div>
     </div> <!-- /page -->
   </div> <!-- /container -->

metadata

@@ -1,79 +1,61 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: sequenceserver
-version: !ruby/object:Gem::Version 
-  hash: 13
+version: !ruby/object:Gem::Version
+  version: 0.7.8
   prerelease: 
-  segments: 
-  - 0
-  - 7
-  - 7
-  version: 0.7.7
 platform: ruby
-authors: 
+authors:
 - Anurag Priyam
 - Ben J Woodcroft
 - Yannick Wurm
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-02-16 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-02-21 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: bundler
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &21083000 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: sinatra
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *21083000
+- !ruby/object:Gem::Dependency
+  name: sinatra
+  requirement: &21082380 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 1
-        - 2
-        - 0
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.2.0
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: ptools
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *21082380
+- !ruby/object:Gem::Dependency
+  name: ptools
+  requirement: &21081860 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id003
-description: |
-  SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
+  prerelease: false
+  version_requirements: *21081860
+description: ! 'SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
+  user interface for use locally or over the web.
 
+'
 email: anurag08priyam@gmail.com
-executables: 
+executables:
 - sequenceserver
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
 - lib/sequenceserver.rb
 - lib/sequenceserver/database_formatter.rb
 - lib/sequenceserver/sequencehelpers.rb
@@ -114,49 +96,31 @@ files:
 - sequenceserver.gemspec
 - bin/sequenceserver
 homepage: http://sequenceserver.com
-licenses: 
+licenses:
 - SequenceServer (custom)
-post_install_message: |+
-  
-  ------------------------------------------------------------------------
-    Thank you for installing SequenceServer :)!
-  
-    To launch SequenceServer execute 'sequenceserver' from command line.
-  
-      $ sequenceserver
-  
-  
-    Visit http://sequenceserver.com for more.
-  ------------------------------------------------------------------------
-  
+post_install_message: ! "\n------------------------------------------------------------------------\n
+  \ Thank you for installing SequenceServer :)!\n\n  To launch SequenceServer execute
+  'sequenceserver' from command line.\n\n    $ sequenceserver\n\n\n  Visit http://sequenceserver.com
+  for more.\n------------------------------------------------------------------------\n\n"
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: iPod of BLAST searching
 test_files: []
-