bio-cnls_screenscraper 0.1.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+end

data/LICENSE.txt

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+Copyright (c) 2011 Ben J. Woodcroft
+
+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 above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+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.

data/README.rdoc

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+= bio-cnls_screenscraper
+
+Description goes here.
+
+== Contributing to bio-cnls_screenscraper
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 Ben J. Woodcroft. See LICENSE.txt for
+further details.
+

data/Rakefile

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-cnls_screenscraper"
+  gem.homepage = "http://github.com/wwood/bioruby-cnls_screenscraper"
+  gem.license = "MIT"
+  gem.summary = %Q{Programmatic interface to the cNLS nuclear localisation signal prediction software}
+  gem.description = %Q{Programmatic interface to the cNLS nuclear localisation signal prediction software}
+  gem.email = "donttrustben@gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
+  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
+  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-cnls_screenscraper #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/bio-cnls_screenscraper.rb

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+#!/usr/bin/env ruby
+
+# A script to take a FASTA file, remove sequences that will fail, and automatically submit it to the cNLS server at http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi
+# Unfortunately, the fasta upload seems to fail. 
+# and format it so that it can be uploaded to the cNLS mapper (classical(?) nuclear localisation signal mapper).
+# The fasta output file can be uploaded to
+# http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi
+
+require 'bio'
+
+module Bio
+  class CNLS
+    class Result
+      attr_accessor :signals
+      
+      def initialize
+        @signals = []
+      end
+      
+      class NLS
+        attr_accessor :position, :sequence, :score
+        
+        # sort by score descending
+        def <=>(another)
+          -(@score<=>another.score)
+        end
+      end
+      class MonopartiteNLS<NLS; end
+      class BipartiteNLS<NLS; end
+      
+      # Is this result a positive prediction or negative prediction?
+      def predicted?
+        !signals.nil? and !signals.empty? 
+      end
+      
+      def monopartite_predicted?(minimum_score=nil)
+        @signals.each do |s|
+          if s.kind_of?(MonopartiteNLS)
+            return true if minimum_score.nil? #if no cutoff, return true
+            return true if s.score >= minimum_score #otherwise apply the cutoff
+          end
+        end
+        return false
+      end
+      
+      def bipartite_predicted?(minimum_score=nil)
+        @signals.each do |s|
+          if s.kind_of?(BipartiteNLS)
+            return true if minimum_score.nil? #if no cutoff, return true
+            return true if s.score >= minimum_score #otherwise apply the cutoff
+          end
+        end
+        return false
+      end
+      
+      def max_monopartite_score
+        max = 0.0
+        @signals.each do |s|
+          if s.kind_of?(MonopartiteNLS) and s.score > max
+            max = s.score
+          end
+        end
+        return max
+      end
+      
+      def max_bipartite_score
+        max = 0.0
+        @signals.each do |s|
+          if s.kind_of?(BipartiteNLS) and s.score > max
+            max = s.score
+          end
+        end
+        return max
+      end
+    end
+    
+    # A class used to automatically submit results to the cNLS webserver and parse the HTML results. 
+    class Screenscraper
+      require 'uri'
+      require 'net/http'
+      
+      ACCEPTABLE_CUTOFFS = %w(2.0 3.0 4.0 5.0 6.0)
+      
+      # Contact the cNLS prediction server and submit the amino acid sequence for prediction. Return a Bio::CNLS::Result object. Pause after each round for pause milliseconds, so as not to overload the server.
+      def self.submit(amino_acid_sequence, cut_off='3.0', seconds_pause=1)
+        # contact webserver and sleep
+        html = get_raw_html_result(amino_acid_sequence, cut_off, seconds_pause)
+        
+        # Return the parsed HTML as a CNLS::Result object
+        return parse_html_result(html)
+      end
+      
+      def self.get_raw_html_result(amino_acid_sequence, cut_off='3.0', seconds_pause=1)
+        unless ACCEPTABLE_CUTOFFS.include?(cut_off)
+          raise Exception, "Specified cutoff `#{cut_off}' for the cNLS screenscraper is invalid. Valid cutoffs are #{ACCEPTABLE_CUTOFFS.join(', ')}. They are strings, not floating point values."
+        end
+        
+        # retrieve the webpage
+        res = Net::HTTP.post_form(URI.parse('http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_y.cgi'),
+        {'cut_off' => cut_off, 'typedseq' => amino_acid_sequence})
+        
+        # if there is an error, raise it
+        unless res.kind_of?(Net::HTTPOK)
+          raise Exception, "Failed to retrieve cNLS, internet connectivity problem? Using cutoff/sequence #{cutoff}/#{amino_acid_sequence}"
+        end
+        
+        # pause the specified number of seconds
+        sleep seconds_pause
+        
+        return res.body
+      end
+      
+      # Given HTML corresponding to a result, return a parse object that is more programmatically palatable.
+      def self.parse_html_result(html)
+        result = Result.new
+        
+        # The mono and bi-partite regular expressions are equivalent except for the Predicted X NLS bit at the beginning, thanksfully. However, they sometimes appear to be slightly different, which is rather odd.
+        monopartite_regex = /Predicted monopartite NLS<\/th>\s+<\/TR>\s*<TR bgcolor="#d0d0d0">\s*<th>Pos.<\/th>\s*<th>Sequence<\/th>\s*<th>Score<\/th>\s*<\/TR>\s*<TR><td><strong><big><code>(.*?)<\/code><\/big><\/strong><br.{0,2}><strong><big><code.{2,8}><\/big><\/strong><\/td><td><strong><big><code>(.*?)<\/code><\/big><\/strong><br.{0,2}><strong><big><code.{2,8}><\/big><\/strong><\/td><td align="center"><strong><big><code>(.*?)<\/code><\/big><\/strong><br.{0,2}><strong><big><code.{2,8}><\/big><\/strong><\/td><\/TR>/i
+        bipartite_regex =     /Predicted bipartite NLS<\/th>\s+<\/TR>\s*<TR bgcolor="#d0d0d0">\s*<th>Pos.<\/th>\s*<th>Sequence<\/th>\s*<th>Score<\/th>\s*<\/TR>\s*<TR><td><strong><big><code>(.*?)<\/code><\/big><\/strong><br.{0,2}><strong><big><code.{2,8}><\/big><\/strong><\/td><td><strong><big><code>(.*?)<\/code><\/big><\/strong><br.{0,2}><strong><big><code.{2,8}><\/big><\/strong><\/td><td align="center"><strong><big><code>(.*?)<\/code><\/big><\/strong><br.{0,2}><strong><big><code.{2,8}><\/big><\/strong><\/td><\/TR>/i
+        
+        monopartite_no_hits = /Predicted monopartite NLS<\/th>\s*<\/tr>\s*<tr bgcolor="#d0d0d0">\s*<th>Pos.<\/th>\s*<th>Sequence<\/th>\s*<th>Score<\/th>\s*<\/tr>\s*<tr><td><strong><big><code><\/code><\/big><\/strong><\/td><td><strong><big><code><\/code><\/big><\/strong><\/td><td align="center"><strong><big><code><\/code><\/big><\/strong><\/td><\/tr>/i
+        bipartite_no_hits =     /Predicted bipartite NLS<\/th>\s*<\/tr>\s*<tr bgcolor="#d0d0d0">\s*<th>Pos.<\/th>\s*<th>Sequence<\/th>\s*<th>Score<\/th>\s*<\/tr>\s*<tr><td><strong><big><code><\/code><\/big><\/strong><\/td><td><strong><big><code><\/code><\/big><\/strong><\/td><td align="center"><strong><big><code><\/code><\/big><\/strong><\/td><\/tr>/i
+        monopartite_no_hits2 = /Predicted monopartite NLS<\/th>\s*<\/TR>\s*<TR bgcolor="#d0d0d0">\s*<th>Pos.<\/th>\s*<th>Sequence<\/th>\s*<th>Score<\/th>\s*<\/TR>\s*<TR><td><strong><big><code \/><\/big><\/strong><\/td><td><strong><big><code \/><\/big><\/strong><\/td><td align="center"><strong><big><code \/><\/big><\/strong><\/td><\/TR>/i
+        bipartite_no_hits2 =     /Predicted bipartite NLS<\/th>\s*<\/TR>\s*<TR bgcolor="#d0d0d0">\s*<th>Pos.<\/th>\s*<th>Sequence<\/th>\s*<th>Score<\/th>\s*<\/TR>\s*<TR><td><strong><big><code \/><\/big><\/strong><\/td><td><strong><big><code \/><\/big><\/strong><\/td><td align="center"><strong><big><code \/><\/big><\/strong><\/td><\/TR>/i
+        
+        split_regex = /<\/code><\/big><\/strong><br.{0,2}><strong><big><code>/
+        
+        # Make sure the sequence isn't too long
+        if html.match(/Query sequence should be < 5000 aa/)
+          raise Exception, "Query sequence provided was too long (> 5000 aa)"
+          
+          # parse out monopartite signals
+        elsif matches = html.match(monopartite_regex)
+          positions = matches[1].split(split_regex)
+          seqs = matches[2].split(split_regex)
+          scores = matches[3].split(split_regex)
+          
+          positions.each_with_index do |pos, i|
+            nls = Result::MonopartiteNLS.new
+            nls.position = pos.to_i
+            nls.sequence = seqs[i]
+            nls.score = scores[i].to_f
+            result.signals.push nls
+          end
+        elsif html.match(monopartite_no_hits) or html.match(monopartite_no_hits2)
+          # do nothing, except for not raising a parsing exception
+        else
+          raise Exception, "Could not parse HTML output returned from cNLS prediction server. In particular, looking for monopartite signals, but the whole document is likely problematic.\n#{html}"
+        end
+        
+        
+        # parse out the bipartite signals
+        if matches = html.match(bipartite_regex)
+          positions = matches[1].split(split_regex)
+          seqs = matches[2].split(split_regex)
+          scores = matches[3].split(split_regex)
+          
+          positions.each_with_index do |pos, i|
+            nls = Result::BipartiteNLS.new
+            nls.position = pos.to_i
+            nls.sequence = seqs[i]
+            nls.score = scores[i].to_f
+            result.signals.push nls
+          end
+        elsif html.match(bipartite_no_hits) or html.match(bipartite_no_hits2)
+          # do nothing, except for not raising a parsing exception
+        else
+          raise Exception, "Could not parse HTML output returned from cNLS prediction server. In particular, looking for bipartite signals, monopartite signals seemed to be parsed OK.\n#{html}"
+        end
+        
+        return result
+      end
+    end
+  end
+end  
+
+
+
+if __FILE__ == $0
+  require 'optparse'
+  
+  # When entering sequences less than this number of amino acids as a query
+  # it fails (if less than 10 it tells you, if less than 19 then it silently fails)
+  QUERY_LENGTH_MINIMUM = 19
+  ACCEPTABLE_AMINO_ACID_CHARACTERS = Bio::AminoAcid::Data::WEIGHT.keys.push('*')
+  
+  options = {
+  :verbose => true,
+  :cache_html => false,
+  :use_cache => false,
+  :cutoff_score => nil,
+  :print_scores => false,
+  }
+  o = OptionParser.new do |opts|
+    opts.banner = [
+    'Usage: bio-cnls_formatter.rb [-qh] [fasta_filename]',
+    '\tfasta file can also be piped in on STDIN.'
+    ]
+    opts.on('-q','--quiet','Opposite of verbose. Default is not quiet (verbose is on)') do
+      options[:verbose] = false
+    end
+    opts.on('-h','--html','Cache HTML results in the current directory instead of parsing them. Default false.') do
+      options[:cache_html] = true
+    end
+    opts.on('-c','--cached','Parse the cache HTML results (as previously generated using -h/--html) in the current directory. Default false.') do
+      options[:use_cache] = true
+    end
+    opts.on('-s','--score SCORE','Cutoff score to be used when parsing results, between 0 and 10. Used when parsing results, not when querying the server') do |s|
+      options[:cutoff_score] = s.to_f
+    end
+    opts.on('-p','--print-scores','Output scores as well as true/false predictions. Default false.') do |s|
+      options[:print_scores] = true
+    end
+  end
+  o.parse!
+  
+  print_result_headers = lambda do
+    to_print = [
+    'Name',
+    'Monopartite signal?',
+    'Bipartite signal?'
+    ]
+    if options[:print_scores]
+      to_print.push 'Max monopartite score'
+      to_print.push 'Max bipartite score'
+    end
+    
+    puts to_print.join("\t")
+  end
+  
+  # Define a procedure for printing parsed results so it is more DRY
+  print_parsed_results = lambda do |sequence_name, cnls_result, score|
+    to_print = [
+    sequence_name,
+    cnls_result.monopartite_predicted?(score),
+    cnls_result.bipartite_predicted?(score)
+    ]
+    if options[:print_scores]
+      to_print.push cnls_result.max_monopartite_score
+      to_print.push cnls_result.max_bipartite_score
+    end
+    
+    puts to_print.join("\t")
+  end
+  
+  # If 
+  if options[:use_cache]
+    print_result_headers.call
+    Dir.foreach('.') do |file|
+      next if File.directory?(file) #skip '.', '..' etc.
+      
+      begin
+        res = Bio::CNLS::Screenscraper.parse_html_result(File.read(file))
+        print_parsed_results.call(
+                                  file, res, options[:cutoff_score]
+        )
+      rescue Exception => e
+        $stderr.puts "Failed to parse #{file}: #{e}"
+      end
+    end
+  else
+    Bio::FlatFile.foreach(ARGF) do |entry|
+      # Sequences are automatically disqualified if they contain characters that are neither amino acids or stop codons
+      fails = entry.seq.gsub(/[#{ACCEPTABLE_AMINO_ACID_CHARACTERS.join('')}]/,'')
+      if fails.length > 0
+        if options[:verbose]
+          $stderr.puts "Found unacceptable characters in #{entry.definition}: #{fails}"
+        end
+        next
+        
+        # Sequence length must be greater than the minimum, excluding
+        # stop codons
+      elsif entry.seq.gsub(/\*/,'').length < QUERY_LENGTH_MINIMUM
+        if options[:verbose]
+          $stderr.puts "Query sequence too short (less than #{QUERY_LENGTH_MINIMUM} residues excluding stop codons): #{entry.definition}"
+        end
+      else
+        # This sequence passes, run the prediction on it
+        if options[:cache_html]
+          res = Bio::CNLS::Screenscraper.get_raw_html_result(entry.seq)
+          File.open("#{entry.definition}.html",'w') do |f|
+            f.puts res
+          end
+          $stderr.print '.' if options[:verbose]
+        else
+          res = Bio::CNLS::Screenscraper.submit(entry.seq)
+          print_result_headers.call
+          print_parsed_results.call(entry, res, options[:cutoff_score])
+        end
+      end
+    end
+  end
+end

data/test/data/badCharacters.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xml:lang="en-US" xmlns="http://www.w3.org/1999/xhtml" lang="en-US"><head>
+<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
+
+<title>NLS Mapper</title>
+<style type="text/css">
+<!--/* <![CDATA[ */
+<!--
+	h2 {color: #B22222; face: Verdana;}
+	.align2 {line-height: 0%;}
+-->
+
+
+/* ]]> */-->
+</style>
+</head><body><p align="center"><b><font #990033="" size="5" color="#b22222" face="Helvetica, Tahoma">cNLS Mapper Result</font></b></p><hr size="5">Error in sequence; your sequence contains an illegal amino acid letter(s).<hr></body></html>

data/test/data/bipartiteHitOnly.html

@@ -0,0 +1,47 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xml:lang="en-US" xmlns="http://www.w3.org/1999/xhtml" lang="en-US"><head>
+<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
+
+<title>NLS Mapper</title>
+<style type="text/css">
+<!--/* <![CDATA[ */
+<!--
+	h2 {color: #B22222; face: Verdana;}
+	.align2 {line-height: 0%;}
+-->
+
+
+/* ]]> */-->
+</style>
+</head><body><p align="center"><b><font #990033="" size="5" color="#b22222" face="Helvetica, Tahoma">cNLS Mapper Result</font></b></p><hr size="5"><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="1" align="center" bgcolor="whitesmoke" border="4">
+	<tbody>
+		<tr bgcolor="#d0d0d0">
+			<th>Predicted NLSs in query sequence</th>
+		</tr>
+<tr><td><strong><code><font size="3"><font color="red">K</font><font color="red">K</font><font color="red">K</font><font color="red">R</font><font color="red">R</font><font color="red">R</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">A</font><font color="red">R</font><font color="red">K</font><font color="red">K</font><font color="red">K</font><font color="red">R</font><font color="red">R</font><font color="red">R</font> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 31</font></code></strong></td></tr>	</tbody>
+</table>
+<br><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="0" align="center" bgcolor="white" border="3">
+	<tbody>
+		<tr bgcolor="darkseagreen">
+			<th colspan="3">Predicted monopartite NLS</th>
+		</tr>
+		<tr bgcolor="#d0d0d0">
+			<th>Pos.</th>
+			<th>Sequence</th>
+			<th>Score</th>
+		</tr>
+<tr><td><strong><big><code></code></big></strong></td><td><strong><big><code></code></big></strong></td><td align="center"><strong><big><code></code></big></strong></td></tr>	</tbody>
+</table>
+<br><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="0" align="center" bgcolor="white" border="3">
+	<tbody>
+		<tr bgcolor="darkseagreen">
+			<th colspan="3">Predicted bipartite NLS</th>
+		</tr>
+		<tr bgcolor="#d0d0d0">
+			<th>Pos.</th>
+			<th>Sequence</th>
+			<th>Score</th>
+		</tr>
+<tr><td><strong><big><code>2</code></big></strong><br><strong><big><code>1</code></big></strong><br><strong><big><code></code></big></strong></td><td><strong><big><code>KKRRRAAAAAAAAAAAAAAAAAARKKKR</code></big></strong><br><strong><big><code>KKKRRRAAAAAAAAAAAAAAAAAARKKKRRR</code></big></strong><br><strong><big><code></code></big></strong></td><td align="center"><strong><big><code>6.2</code></big></strong><br><strong><big><code>5</code></big></strong><br><strong><big><code></code></big></strong></td></tr>	</tbody>
+</table>
+<br></body></html>

data/test/data/lessThan10Fail.html

@@ -0,0 +1,16 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xml:lang="en-US" xmlns="http://www.w3.org/1999/xhtml" lang="en-US"><head>
+<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
+
+<title>NLS Mapper</title>
+<style type="text/css">
+<!--/* <![CDATA[ */
+<!--
+	h2 {color: #B22222; face: Verdana;}
+	.align2 {line-height: 0%;}
+-->
+
+
+/* ]]> */-->
+</style>
+</head><body><p align="center"><b><font #990033="" size="5" color="#b22222" face="Helvetica, Tahoma">cNLS Mapper Result</font></b></p><hr size="5">Query sequence should be &gt; 10 aa.<hr></body></html>

data/test/data/monopartiteHitOnly.html

@@ -0,0 +1,50 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xml:lang="en-US" xmlns="http://www.w3.org/1999/xhtml" lang="en-US"><head>
+<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
+
+<title>NLS Mapper</title>
+<style type="text/css">
+<!--/* <![CDATA[ */
+<!--
+	h2 {color: #B22222; face: Verdana;}
+	.align2 {line-height: 0%;}
+-->
+
+
+/* ]]> */-->
+</style>
+</head><body><p align="center"><b><font #990033="" size="5" color="#b22222" face="Helvetica, Tahoma">cNLS Mapper Result</font></b></p><hr size="5"><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="1" align="center" bgcolor="whitesmoke" border="4">
+	<tbody>
+		<tr bgcolor="#d0d0d0">
+			<th>Predicted NLSs in query sequence</th>
+		</tr>
+<tr><td><strong><code><font size="3"><font color="red">K</font><font color="red">K</font><font color="red">K</font><font color="red">K</font><font color="red">R</font><font color="red">R</font><font color="red">R</font><font color="red">A</font><font color="red">A</font>AAAAAAAAAAAAAAAAAAAAA
+ 
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+ 30</font></code></strong></td></tr>	</tbody>
+</table>
+<br><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="0" align="center" bgcolor="white" border="3">
+	<tbody>
+		<tr bgcolor="darkseagreen">
+			<th colspan="3">Predicted monopartite NLS</th>
+		</tr>
+		<tr bgcolor="#d0d0d0">
+			<th>Pos.</th>
+			<th>Sequence</th>
+			<th>Score</th>
+		</tr>
+<tr><td><strong><big><code>1</code></big></strong><br><strong><big><code></code></big></strong></td><td><strong><big><code>KKKKRRRAA</code></big></strong><br><strong><big><code></code></big></strong></td><td align="center"><strong><big><code>10</code></big></strong><br><strong><big><code></code></big></strong></td></tr>	</tbody>
+</table>
+<br><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="0" align="center" bgcolor="white" border="3">
+	<tbody>
+		<tr bgcolor="darkseagreen">
+			<th colspan="3">Predicted bipartite NLS</th>
+		</tr>
+		<tr bgcolor="#d0d0d0">
+			<th>Pos.</th>
+			<th>Sequence</th>
+			<th>Score</th>
+		</tr>
+<tr><td><strong><big><code></code></big></strong></td><td><strong><big><code></code></big></strong></td><td align="center"><strong><big><code></code></big></strong></td></tr>	</tbody>
+</table>
+<br></body></html>

data/test/data/nohits.html

@@ -0,0 +1,47 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xml:lang="en-US" xmlns="http://www.w3.org/1999/xhtml" lang="en-US"><head>
+<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
+
+<title>NLS Mapper</title>
+<style type="text/css">
+<!--/* <![CDATA[ */
+<!--
+	h2 {color: #B22222; face: Verdana;}
+	.align2 {line-height: 0%;}
+-->
+
+
+/* ]]> */-->
+</style>
+</head><body><p align="center"><b><font #990033="" size="5" color="#b22222" face="Helvetica, Tahoma">cNLS Mapper Result</font></b></p><hr size="5"><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="1" align="center" bgcolor="whitesmoke" border="4">
+	<tbody>
+		<tr bgcolor="#d0d0d0">
+			<th>Predicted NLSs in query sequence</th>
+		</tr>
+<tr><td><strong><code><font size="3">AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 40</font></code></strong></td></tr>	</tbody>
+</table>
+<br><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="0" align="center" bgcolor="white" border="3">
+	<tbody>
+		<tr bgcolor="darkseagreen">
+			<th colspan="3">Predicted monopartite NLS</th>
+		</tr>
+		<tr bgcolor="#d0d0d0">
+			<th>Pos.</th>
+			<th>Sequence</th>
+			<th>Score</th>
+		</tr>
+<tr><td><strong><big><code></code></big></strong></td><td><strong><big><code></code></big></strong></td><td align="center"><strong><big><code></code></big></strong></td></tr>	</tbody>
+</table>
+<br><table bordercolorlight="darkgray" bordercolordark="darkslategray" cellpadding="5" cellspacing="0" align="center" bgcolor="white" border="3">
+	<tbody>
+		<tr bgcolor="darkseagreen">
+			<th colspan="3">Predicted bipartite NLS</th>
+		</tr>
+		<tr bgcolor="#d0d0d0">
+			<th>Pos.</th>
+			<th>Sequence</th>
+			<th>Score</th>
+		</tr>
+<tr><td><strong><big><code></code></big></strong></td><td><strong><big><code></code></big></strong></td><td align="center"><strong><big><code></code></big></strong></td></tr>	</tbody>
+</table>
+<br></body></html>

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-cnls_screenscraper'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-cnls_screenscraper.rb

@@ -0,0 +1,40 @@
+require 'helper'
+require 'bio-cnls_screenscraper'
+
+class TestBioCnlsScreenscraper < Test::Unit::TestCase
+  @@data_dir = File.join(File.dirname(__FILE__),['data'])
+ 
+  should "correctly parse hit results with no hits" do
+    html = File.open(File.join(@@data_dir,'nohits.html')).read
+    result = Bio::CNLS::Screenscraper.parse_html_result(html)
+    assert_equal [], result.signals
+  end
+  
+  should "correctly parse bipartite-only signals page" do
+    html = File.open(File.join(@@data_dir,'bipartiteHitOnly.html')).read
+    result = Bio::CNLS::Screenscraper.parse_html_result(html)
+    assert_equal 2, result.signals.length
+    assert_equal 'KKKRRRAAAAAAAAAAAAAAAAAARKKKRRR', result.signals.sort[1].sequence
+    assert_equal 5.0, result.signals.sort[1].score
+    assert_equal 1, result.signals.sort[1].position
+  end
+  
+  should "correctly parse results with monopartite signals only" do
+    html = File.open(File.join(@@data_dir,'monopartiteHitOnly.html')).read
+    result = Bio::CNLS::Screenscraper.parse_html_result(html)
+    assert_equal 1, result.signals.length
+    assert_equal 'KKKKRRRAA', result.signals.sort[0].sequence
+    assert_equal 10.0, result.signals.sort[0].score
+    assert_equal 1, result.signals.sort[0].position
+  end
+  
+  should "apply the correct monopartite cutoff" do
+    nls = Bio::CNLS::Result::MonopartiteNLS.new
+    nls.score = 8.0
+    result = Bio::CNLS::Result.new
+    result.signals.push nls
+    assert_equal true, result.monopartite_predicted?(7.0)
+    assert_equal true, result.monopartite_predicted?(8.0)
+    assert_equal false, result.monopartite_predicted?(9.0)
+  end
+end

metadata

@@ -0,0 +1,157 @@
+--- !ruby/object:Gem::Specification 
+name: bio-cnls_screenscraper
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-02-21 00:00:00 +11:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: shoulda
+  type: :development
+  version_requirements: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  requirement: *id001
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: bundler
+  type: :development
+  version_requirements: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  requirement: *id002
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: jeweler
+  type: :development
+  version_requirements: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 1
+        - 5
+        - 2
+        version: 1.5.2
+  requirement: *id003
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: rcov
+  type: :development
+  version_requirements: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  requirement: *id004
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: bio
+  type: :development
+  version_requirements: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 5
+        segments: 
+        - 1
+        - 4
+        - 1
+        version: 1.4.1
+  requirement: *id005
+description: Programmatic interface to the cNLS nuclear localisation signal prediction software
+email: donttrustben@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-cnls_screenscraper.rb
+- test/data/badCharacters.html
+- test/data/bipartiteHitOnly.html
+- test/data/lessThan10Fail.html
+- test/data/monopartiteHitOnly.html
+- test/data/nohits.html
+- test/helper.rb
+- test/test_bio-cnls_screenscraper.rb
+has_rdoc: true
+homepage: http://github.com/wwood/bioruby-cnls_screenscraper
+licenses: 
+- MIT
+post_install_message: 
+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: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Programmatic interface to the cNLS nuclear localisation signal prediction software
+test_files: 
+- test/helper.rb
+- test/test_bio-cnls_screenscraper.rb