sequenceserver 0.7.6 → 0.7.7

data/lib/sequenceserver/customisation.rb

@@ -1,60 +1,104 @@
 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
 
-    ## 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
+    # 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
   end
-end
+end

data/lib/sequenceserver/sequencehelpers.rb

@@ -94,7 +94,7 @@ module SequenceServer
       #
       # If `blastdbcmd` throws error, we assume sequence not found.
       blastdbcmd = settings.binaries['blastdbcmd']
-      command = %x|#{blastdbcmd} -db #{db} -entry #{ids} 2> /dev/null|
+      %x|#{blastdbcmd} -db #{db} -entry '#{ids}' 2> /dev/null|
     end
 
     # Given a sequence_id and databases, apply the default (standard)

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.7.6'
+  s.version     = '0.7.7'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'

data/views/search.erb

@@ -1,12 +1,13 @@
 <!DOCTYPE html>
 <html lang="en">
 <head>
-  <title>SequenceServer: Custom BLAST Server</title>
+  <title>Fourmidable: BLAST ant genomes, proteomes, and transcriptomes.</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="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
+  <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 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>
@@ -17,13 +18,27 @@
   <%# 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 Sequence(s)</h1>
+        <h1>BLAST Ant Genomes(s)</h1>
       </div>
 
       <form method="post" action="<%= uri('/#result') %>">
@@ -216,7 +231,8 @@
       </div>
 
       <div id="underbar">
-        <p>&copy; <a href='http://www.sequenceserver.com'>SequenceServer: BLAST search made easy!</a></p>
+        <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>
       </div>
     </div> <!-- /page -->
   </div> <!-- /container -->

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: sequenceserver
 version: !ruby/object:Gem::Version 
-  hash: 15
+  hash: 13
   prerelease: 
   segments: 
   - 0
   - 7
-  - 6
-  version: 0.7.6
+  - 7
+  version: 0.7.7
 platform: ruby
 authors: 
 - Anurag Priyam
@@ -17,7 +17,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-02-12 00:00:00 Z
+date: 2012-02-16 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: bundler
@@ -84,12 +84,12 @@ files:
 - lib/sequenceserver/database.rb
 - views/search.erb
 - views/500.erb
+- public/favicon.ico
 - public/blastResult.js
 - public/css/bootstrap.min.css
 - public/css/custom.css
 - public/js/jquery.js
 - public/js/jquery.enablePlaceholder.min.js
-- public/js/liveclip.jquery.js
 - public/js/sequenceserver.js
 - public/js/jquery.activity.js
 - public/js/sequenceserver.blast.js

data/public/js/liveclip.jquery.js

@@ -1,246 +0,0 @@
-/**
- * jQuery Live Clipboard
- *
- * Copyright (c) 2009 Shinichi Tomita (shinichi.tomita@gmail.com)
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- */
-(function($) {
-
-  var namespace = 'liveclip';
-  var relayEvents = 
-    'click,dblclick,mousedown,mouseup,mousemove,mouseover,mouseout,keypress,keyup'.split(',');
-
-  /**
-   * Adjust clipboard textarea size to cover parent clippable element.
-   */
-  function track() {
-    var target = $(this);
-    var clipboard = target.clipboard();
-    var w = target.outerWidth(), h = target.outerHeight(), offset = target.offset();
-    if (/^(auto|scroll)$/.test(target.css('overflow'))) w -= 20;
-    if (clipboard) clipboard.css({ width : w, height : h, top : offset.top, left : offset.left });
-  }
-
-  /**
-   * Finding and capture event target element, excluding clipboard textarea.
-   * This is "pseudo" capturing, assuming no layered elements covering over the target.
-   */
-  function capture(el, e) {
-    var captured = _capture(el);
-    var clipboard = captured.clipboard();
-    // if captured element has clipboard, return it. 
-    return captured !== el && clipboard ? clipboard : captured;
-
-    function _capture(el) {
-      var target = el;
-      el.children().each(function() {
-        var child = $(this);
-        var w = child.width(), h = child.innerHeight(), offset = child.offset();
-        if (e.pageX > offset.left && e.pageX < offset.left + w &&
-            e.pageY > offset.top  && e.pageY < offset.top  + h) {
-          target = _capture(child);
-        }
-      })
-      return target;
-    }
-  }
-
-  /**
-   * Context menu event handler 
-   */
-  function contextmenuHandler(e) {
-    var clipboard = $(this);
-    var target = clipboard.data(namespace + '-target');
-    var options = target.data(namespace + '-clipboard-options');
-
-    if (options.active && options.active.call(target) === false) {
-      clipboard.attr('readonly', 'readonly');
-      return;
-    }
-
-    if (options.paste || options.del) {
-      clipboard.removeAttr('readonly');
-    } else {
-      clipboard.attr('readonly', 'readonly');
-    }
-
-    var val = options.copy ? options.copy.call(target) : '';
-    clipboard.val(val);
-    clipboard.get(0).select(); 
-    if (options.paste || options.del) {
-      val = clipboard.val();
-      var watchPID = clipboard.data(namespace+'-watcher');
-      if (watchPID) {
-        clearInterval(watchPID);
-        clipboard.removeData(namespace+'-watcher');
-      }
-      watchPID = setInterval(function() {
-        var v = clipboard.val();
-        if (v !== val) {
-          try {
-            if (v === '') {
-              if (options.del) options.del.call(target)
-            } else {
-              if (options.paste) options.paste.call(target, v);
-              clipboard.val('');
-            }
-          } catch(e) {}
-          clearInterval(watchPID);
-          clipboard.removeData(namespace+'-watcher');
-        }
-      }, 100);
-      clipboard.data(namespace+'-watcher', watchPID);
-    }
-  }
-
-
-  /**
-   * Keyboard down event handler
-   */
-  function keydownHandler(e) {
-    var clipboard = $(this);
-    var target = clipboard.data(namespace + '-target');
-    var options = target.data(namespace + '-clipboard-options');
-
-    if (e.metaKey) {
-      switch (e.keyCode) {
-        case 67 : // Command + C
-          var val = options.copy ? options.copy.call(target) : '';
-          clipboard.val(val)
-          clipboard.get(0).select(); 
-          break;
-        case 86 : // Command + V
-          if (options.paste) {
-            clipboard.get(0).select(); 
-            setTimeout(function() {
-              var data = clipboard.val();
-              options.paste.call(target, data);
-              clipboard.val('')
-            }, 10);
-          }
-          break;
-        case 88 : // Command + X
-          var val = options.copy ? options.copy.call(target) : '';
-          clipboard.val(val)
-          clipboard.get(0).select(); 
-          if (options.del) {
-            setTimeout(function() {
-              options.del.call(target)
-            }, 10);
-          }
-          break;
-        default :
-          break;
-      }
-    } else if (e.keyCode==46) { // delete
-      if (options.del) options.del.call(target);
-    }
-
-  }
-
-
-  $.fn.extend({
-
-    /**
-     * Attach clipboard feature to block element
-     * Get current clipboard proxy textarea
-     */
-    clipboard : function(options) {
-      var elements = this;
-
-      if (options) { // setter
-
-        $(elements).each(function() {
-          var target = $(this);
-          var clipboard = target.data(namespace + '-clipboard');
-          if (!clipboard) { 
-            clipboard = $('<textarea></textarea>')
-              .addClass(namespace+'-clipboard')
-              .addClass(options.cls ? options.cls : '')
-              .css({ 
-                cursor : 'default',
-                position : 'absolute', 
-                fontSize : $.liveclip.debug ? '12px' : '1px',
-                opacity : $.liveclip.debug ? .5 : .01 
-              })
-              .appendTo(document.body)
-              .bind('contextmenu', contextmenuHandler)
-              .bind('keydown', keydownHandler);
-            $.each(relayEvents, function(i, eventName) {
-              clipboard.bind(eventName+'.'+namespace, function(e) { 
-                capture(target, e).trigger(e);
-              });
-            });
-            if ($.liveclip.autoTrack) { target.bind('mouseover.'+namespace, track) }
-            target.data(namespace+'-clipboard', clipboard);
-            clipboard.data(namespace+'-target', target);
-          }
-          target.data(namespace+'-clipboard-options', options);
-          track.call(target);
-        });
-        return this;
-
-      } else { // getter
-        return $(this).data(namespace + '-clipboard');
-      }
-
-    }
-    ,
-
-    /**
-     * remove attached clipboard feature
-     */
-    removeClipboard : function() {
-      $(this).each(function() {
-        $(this).clipboard().remove();
-        $(this).unbind('mouseover.'+namespace, track)
-               .removeData(namespace + '-clipboard')
-               .removeData(namespace + '-clipboard-options');
-      });
-      return this;
-    }
-
-  });
-
-  $.liveclip = {
-    debug : false,
-    autoTrack : false
-  }
-
-  /**
-   * Track all clipboard, aligning to target element position and size
-   * If no target element available in document, removing clipboard.
-   */
-  $.trackClipboards = function() {
-    $('body > textarea.'+namespace+'-clipboard').each(function() {
-      var clipboard = $(this);
-      var target = clipboard.data(namespace + '-target');
-      if (target && target.parent()) {
-        track.call(target);
-      } else {
-        clipboard.remove();
-      }
-    });
-  }
-
-  $(function() {
-    if ($.liveclip.autoTrack) {
-      $(document).mousemove($.trackClipboards);
-    }
-  })
-
-})(jQuery)