sequenceserver 0.6.7

data/tests/test_sequencehelpers.rb

@@ -0,0 +1,85 @@
+#!/usr/bin/env ruby 
+# test_ssequencehelpers.rb
+
+# ensure 'lib/' is in the load path
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+
+require 'sequenceserver'
+require 'sequenceserver/sequencehelpers'
+require 'test/unit'
+
+
+
+class Tester < Test::Unit::TestCase
+  include SequenceServer::SequenceHelpers
+  def test_guess_sequence_type_nucleotide
+  #must 'correctly detect nucleotide sequence, even when it includes crap' do   
+    ['AAAAAAAAAAAAAAAAAAAAAT',
+     '           CAGATGCRRCAAAGCAAACGGCAA 34523453 652352',
+     'ACCNNNNNNXXXXCAUUUUUU',
+     "ACGT\n\t\t\nACCACGGACCACGAAAGCG"               ].each do |seq|
+      assert_equal(:nucleotide, guess_sequence_type(seq), message="for #{seq}")
+    end
+  end
+
+  def test_guess_sequence_type_aminoacid
+  #must 'correctly detect aminoacid sequence, even when it includes a lot of crap' do
+  ['ADSACGHKSJLFCVMGTL',
+   '  345   KSSYPHYSPPPPHS      345 23453 652352',
+   'GEYSNLNNNNNNXXXXSSSSSSSSSSSSSSSSSSSSSSS',
+   "EE\n\t\t\n         \t\t\EEQRRQQSARTSRRQR"     ].each do |seq|
+      assert_equal(:protein, guess_sequence_type(seq) , message="for #{seq}")
+    end
+  end
+
+  def test_guess_sequence_type_impossible
+    assert_equal(nil, guess_sequence_type('ACSFGT'), message='too little sequence')
+  end
+
+  ## Tests for type_of_sequences  (multi-fasta  kind of thing the user would enter)
+  def test_type_of_sequences
+    aa_multifasta = ">SDFDSF\nACGTGSDLKJGNLDKSJFLSDKJFLSDKOIU\n>asdfas\nasfasdfffffffffffffffffffff\n>alksjflkasdj slakdjf\nasdfasdfasdfljaslkdjf"
+    aa_multifasta_including_short_seq_missing_lead = "ACGTGSDLKJGNLDKSJFLSDKJFLSDKOIU\n>asdfas\nasf\n>alksjflkasdj slakdjf\nasdfasdfasdfljaslkdjf"
+    aa_singlesequence =  "ACGTGSDLKJGNLDKSJFLSDKJFLSDKOIU\n"
+    nt_multifasta = ">asdf\nAAAAAAAAAAAAAAAAAAAAT\n>sfaslkj\nCAGATGCRRCAAAGCAAACGGCAA\n>asssssjlkj\nACCCANNNNNNXXXXCAUUUUUU"
+    aa_nt_mix = ">alksjflkasdj slakdjf\nasdfasdfasdfljaslkdjf\n>ffffffassdf\nACGCNAGTGCCCCCCCCGANATGGGTGGTTXXXXXGGTG"
+
+    assert_equal(:protein, type_of_sequences(aa_multifasta), 'aa_multifasta')
+    assert_equal(:protein, type_of_sequences(aa_multifasta_including_short_seq_missing_lead ), 'aa_multifasta_short_seq_and_no_>')
+    assert_equal(:protein, type_of_sequences(aa_singlesequence), 'single AA sequence')
+    assert_equal(:nucleotide, type_of_sequences(nt_multifasta), 'nt_multifasta')
+    assert_raise(ArgumentError, 'mixed aa and nt should raise') { type_of_sequences(aa_nt_mix) }
+  end
+
+  def test_sequence_type_to_blast_methods
+    assert_equal ['blastp', 'tblastn'], blast_methods_for(:protein), 'blasts_for_protein'
+    assert_equal ['blastn','tblastx','blastx'], blast_methods_for(:nucleotide), 'blasts_for_nucleotide'
+    assert_equal ['blastp', 'tblastn','blastn','tblastx','blastx'], blast_methods_for(nil), 'blasts_for_nil'
+  end
+
+  def test_composition
+    expected_comp = {"a"=>2, "d"=>3, "f"=>7, "s"=>3, "A"=>1}
+    assert_equal(expected_comp, composition('asdfasdfffffAsdf'))
+  end
+  
+  def test_construct_standard_sequence_hyperlink
+    assert_equal "/get_sequence/?id=one&db=abc def", construct_standard_sequence_hyperlink({:sequence_id => 'one', :databases => %w(abc def)})
+    assert_equal nil, construct_standard_sequence_hyperlink({:sequence_id => ' one', :databases =>  %w(abc def)})
+    assert_equal "/get_sequence/?id=MAL13P1.218&db=abc def", construct_standard_sequence_hyperlink({:sequence_id => 'lcl|MAL13P1.218', :databases =>  %w(abc def)})
+  end
+end
+
+class AppTester < Test::Unit::TestCase
+  def test_process_advanced_blast_options
+    # dirty hack, required to work around Sinatra's overriden `new` method that
+    # may return instance of any Rack class
+    app = SequenceServer::App.allocate
+    app.send(:initialize)
+
+    assert_nothing_raised {app.validate_advanced_parameters('')}
+    assert_nothing_raised {app.validate_advanced_parameters('-word_size 5')}
+    assert_raise(ArgumentError, 'security advanced option parser'){app.validate_advanced_parameters('-word_size 5; rm -rf /')}
+    assert_raise(ArgumentError, 'conflicting advanced option'){app.validate_advanced_parameters('-db roar')}
+  end
+end
+

data/views/500.erb

@@ -0,0 +1,22 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xml:lang="en" lang="en" xmlns="http://www.w3.org/1999/xhtml">
+<head>
+    <title>SequenceServer</title>
+    <meta name="author" content="Anurag Priyam" />
+    <meta name="author" content="Yannick Wurm" />
+    <meta name="author" content="Cedric Wurm" />
+    <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
+
+    <%# 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/beige.css') %> />
+</head>
+
+<body>
+  <div class="container">
+    <h1>Oops! Something went wonky!</h1>
+	<p>Apologies, there was an error with your request: 
+	  <strong><%=request.env['sinatra.error'].message %> </strong></p>
+    <p>If the error persists please contact the administrator</p>
+  </div>
+</body>

data/views/search.erb

@@ -0,0 +1,221 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <title>SequenceServer</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 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>
+  <script type="text/javascript" src="<%= uri('/js/search.js') %>"></script>
+
+  <%# 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') %>" />
+</head>
+
+<body>
+  <div class="container">
+    <div class="page">
+      <div class="page-header" id="banner">
+        <h1>BLAST Sequence(s)</h1>
+      </div>
+
+      <form method="post" action="<%= uri('/#result') %>">
+        <div class="row">
+          <div class="span12">
+            <div class="offset-left sequence">
+              <div class="clearfix">
+                <textarea name="sequence" id="sequence" rows="11" placeholder="Paste your sequence(s) here..." ></textarea>
+              </div>
+            </div>
+          </div>
+
+          <div class="span4">
+            <div class="offset-right box blastmethods">
+              <div class="clearfix">
+                <fieldset>
+                  <legend><h4>Blast methods</h4></legend>
+                    <ul class="inputs-list">
+                      <li>
+                        <label title="Protein query; protein database.">
+                          <input type="radio" name="method" value="blastp" id="blastp"/>
+                          <span>blastp</span>
+                        </label>
+                      </li>
+                      <li>
+                        <label title="Protein query; six frame translated nucleotide database.">
+                          <input type="radio" name="method" value="tblastn" id="tblastn"/>
+                          <span>tblastn</span>
+                        </label>
+                      </li>
+                      <li>
+                        <label title="Nucleotide query; nucleotide database.">
+                          <input type="radio" name="method" value="blastn" id="blastn"/>
+                          <span>blastn</span>
+                        </label>
+                      </li>
+                      <li>
+                        <label title="Translated nucleotide query; protein database">
+                          <input type="radio" name="method" value="blastx" id="blastx"/>
+                          <span>blastx</span>
+                        </label>
+                      </li>
+                      <li>
+                        <label title="Six-frame translated nucleotide query; six-frame translated nucleotide database">
+                          <input type="radio" name="method" value="tblastx" id="tblastx"/>
+                          <span>tblastx</span>
+                        </label>
+                      </li>
+                  </ul>
+                </fieldset>
+              </div>
+            </div>
+          </div>
+        </div>
+
+        <div class="row">
+          <div class="span8">
+            <div class="offset-left box databases nucleotide">
+              <div class="clearfix">
+                <fieldset>
+                  <legend><h4>Nucleotide databases</h4></legend>
+                  <ul class="inputs-list">
+                    <% settings.databases['nucleotide'].each_with_index do |db, i| %>
+                      <li>
+                        <label>
+                          <input type="checkbox" id="ndb<%=i%>" name="db[nucleotide][]" value="<%=i%>"/>
+                          <span> <%= db.title or db.name %></span>
+                        </label>
+                      </li>
+                    <% end %>
+                  </ul>
+                </fieldset>
+              </div>
+            </div>
+          </div>
+
+          <div class="span8">
+            <div class="offset-right box databases protein">
+              <div class="clearfix">
+                <fieldset>
+                  <legend><h4>Protein databases</h4></legend>
+                  <ul class="inputs-list">
+                    <% settings.databases['protein'].each_with_index do |db, i| %>
+                      <li>
+                        <label>
+                          <input type="checkbox" id="pdb<%=i%>" name="db[protein][]" value="<%=i%>"/>
+                          <span> <%= db.title or db.name %></span>
+                        </label>
+                      </li>
+                    <% end %>
+                  </ul>
+                </fieldset>
+              </div>
+            </div>
+          </div>
+        </div>
+
+        <div class="row">
+          <div class="span12">
+            <div class="offset-left box advanced">
+              <div class="clearfix">
+                <label class="span4" for="advanced"><h4 title="Click to show/hide advanced options.">Advanced Parameters:</h4></label>
+                <input class="span8" type="text" name="advanced" id="advanced" title="View, and enter advanced parameters." placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
+              </div>
+  <pre class="help">
+  <%= ERB::Util.h %q|
+  -evalue <Real>
+    Expectation value (E) threshold for saving hits
+    Default = `10'
+  -word_size <Integer, >=2>
+    Word size for wordfinder algorithm
+  -gapopen <Integer>
+    Cost to open a gap
+  -gapextend <Integer>
+    Cost to extend a gap
+  -matrix <String>
+    Scoring matrix name (normally BLOSUM62)
+  -threshold <Real, >=0>
+    Minimum word score such that the word is added to the BLAST lookup table
+  -comp_based_stats <String>
+    Use composition-based statistics for blastp / tblastn:
+        D or d: default (equivalent to 2)
+        0 or F or f: no composition-based statistics
+        1: Composition-based statistics as in NAR 29:2994-3005, 2001
+        2 or T or t : Composition-based score adjustment as in Bioinformatics
+    21:902-911,
+        2005, conditioned on sequence properties
+        3: Composition-based score adjustment as in Bioinformatics 21:902-911,
+        2005, unconditionally
+    For programs other than tblastn, must either be absent or be D, F or 0
+    Default = `2'
+  -num_descriptions <Integer, >=0>
+    Number of database sequences to show one-line descriptions for
+    Default = `500'
+  -num_alignments <Integer, >=0>
+    Number of database sequences to show alignments for
+    Default = `250'
+  *** Query filtering options
+  -seg <String>
+    Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
+    'no' to disable)
+    Default = `no'
+  -soft_masking <Boolean>
+    Apply filtering locations as soft masks
+    Default = `false'
+  -lcase_masking
+    Use lower case filtering in query and subject sequence(s)?
+  *** Restrict search or results
+  -gilist <String>
+    Restrict search of database to list of GI's
+      * Incompatible with:  negative_gilist, seqidlist, remote, subject,
+    subject_loc
+  -seqidlist <String>
+    Restrict search of database to list of SeqId's
+      * Incompatible with:  gilist, negative_gilist, remote, subject,
+    subject_loc
+  -negative_gilist <String>
+    Restrict search of database to everything except the listed GIs
+      * Incompatible with:  gilist, seqidlist, remote, subject, subject_loc
+  -entrez_query <String>
+    Restrict search with the given Entrez query
+      * Requires:  remote
+  -db_soft_mask <String>
+    Filtering algorithm ID to apply to the BLAST database as soft masking
+      * Incompatible with:  subject, subject_loc
+  -culling_limit <Integer, >=0>
+    If the query range of a hit is enveloped by that of at least this many
+    higher-scoring hits, delete the hit
+      * Incompatible with:  best_hit_overhang, best_hit_score_edge
+  -best_hit_overhang <Real, (>0 and <0.5)>
+    Best Hit algorithm overhang value (recommended value: 0.1)
+      * Incompatible with:  culling_limit
+  -best_hit_score_edge <Real, (>0 and <0.5)>
+    Best Hit algorithm score edge value (recommended value: 0.1)
+      * Incompatible with:  culling_limit
+  -max_target_seqs <Integer, >=1>
+    Maximum number of aligned sequences to keep | %>
+  </pre>
+          </div>
+        </div>
+
+          <div class="span4">
+            <input type="submit" class="btn large primary" value="BLAST!"/>
+          </div>
+        </div>
+      </form>
+
+      <div id="result" class="offset-left offset-right">
+        <%= @blast %>
+      </div>
+
+      <div id="underbar">
+        <p>&copy; <a href='http://www.sequenceserver.com'>sequenceserver.com</a></p>
+      </div>
+    </div> <!-- /page -->
+  </div> <!-- /container -->
+</body>
+</html>

metadata

@@ -0,0 +1,141 @@
+--- !ruby/object:Gem::Specification 
+name: sequenceserver
+version: !ruby/object:Gem::Version 
+  hash: 9
+  prerelease: 
+  segments: 
+  - 0
+  - 6
+  - 7
+  version: 0.6.7
+platform: ruby
+authors: 
+- Anurag Priyam
+- Ben J Woodcroft
+- Yannick Wurm
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-12-13 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: sinatra
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 15
+        segments: 
+        - 1
+        - 0
+        version: "1.0"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: ptools
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id002
+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: 
+- sequenceserver
+- database_formatter
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- lib/sequenceserver.rb
+- lib/sequenceserver/sequencehelpers.rb
+- lib/sequenceserver/customisation.rb
+- lib/sequenceserver/helpers.rb
+- lib/sequenceserver/sinatralikeloggerformatter.rb
+- lib/sequenceserver/blast.rb
+- lib/sequenceserver/database.rb
+- views/search.erb
+- views/500.erb
+- public/blastResult.js
+- public/css/bootstrap.min.css
+- public/css/custom.css
+- public/js/jquery.js
+- public/js/jquery.enablePlaceholder.min.js
+- public/js/search.js
+- tests/test_sequencehelpers.rb
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
+- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
+- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
+- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
+- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
+- config.ru
+- example.config.yml
+- LICENSE.txt
+- README.txt
+- Gemfile
+- sequenceserver.gemspec
+- bin/sequenceserver
+- bin/database_formatter
+homepage: http://sequenceserver.com
+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.
+  ------------------------------------------------------------------------
+  
+rdoc_options: []
+
+require_paths: 
+- lib
+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 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: iPod of BLAST searching
+test_files: []
+