initial commit, gathering old scattered code

.gitignore

@@ -46,3 +46,7 @@ pkg
 
 # For rubinius:
 #*.rbc
+
+# Because this is a Gem, not an app
+Gemfile.lock
+

README.rdoc

@@ -1,6 +1,8 @@
 = bio-exportpred
 
-Description goes here.
+ExportPred is a computer program for predicting whether particular Plasmodium falciparum proteins are exported into the red blood cell cytosol during the intraerythrocytic stages. This biogem is a wrapper around the program, so that it can be interacted with programmatically.
+
+http://bioinf.wehi.edu.au/exportpred/
 
 == Contributing to bio-exportpred
 

Rakefile

@@ -17,8 +17,8 @@ Jeweler::Tasks.new do |gem|
   gem.name = "bio-exportpred"
   gem.homepage = "http://github.com/wwood/bioruby-exportpred"
   gem.license = "MIT"
-  gem.summary = %Q{TODO: one-line summary of your gem}
-  gem.description = %Q{TODO: longer description of your gem}
+  gem.summary = %Q{Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins}
+  gem.description = %Q{Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins. Requires local install of the program, which is available from http://bioinf.wehi.edu.au/exportpred/}
   gem.email = "donttrustben near gmail.com"
   gem.authors = ["Ben J Woodcroft"]
   # dependencies defined in Gemfile

VERSION

@@ -1 +1 @@
-0.0.0
+0.0.1

bio-exportpred.gemspec

@@ -0,0 +1,60 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-exportpred"
+  s.version = "0.0.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Ben J Woodcroft"]
+  s.date = "2012-01-14"
+  s.description = "TODO: longer description of your gem"
+  s.email = "donttrustben near gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "lib/bio-exportpred.rb",
+    "test/helper.rb",
+    "test/test_bio-exportpred.rb"
+  ]
+  s.homepage = "http://github.com/wwood/bioruby-exportpred"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.14"
+  s.summary = "TODO: one-line summary of your gem"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+  end
+end
+

lib/bio-exportpred.rb

@@ -1,11 +1 @@
-# Please require your code below, respecting the bioruby directory tree. 
-# For instance, perhaps the only uncommented line in this file might 
-# be something like this:
-#
-#   require 'bio/sequence/awesome_sequence_plugin_thingy'
-#
-# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
-# and put your plugin's code there. It is bad practice to write other code 
-# directly into this file, because doing so causes confusion if this biogem 
-# was ever to get merged into the main bioruby tree.
-
+require 'bio/appl/exportpred'

lib/bio/appl/exportpred.rb

@@ -0,0 +1,70 @@
+require 'open3'
+
+module Bio
+  class ExportPred
+    class Wrapper
+      def calculate(sequence)
+        command = 'exportpred --input=-'
+        Open3.popen3(command) do |stdin, stdout, stderr, wait_thr|
+          stdin.puts '>wrapperSeq'
+          stdin.puts "#{sequence}"
+          stdin.close
+
+          result = stdout.readlines
+          error = stderr.readlines
+
+          unless error.length == 1
+            raise Exception, "There appears to be a problem while running ExportPred:\n#{error}"
+          end
+          parse_error = error[0].strip.match(/^(\d+) sequences read from stdin$/)
+          unless parse_error[1].to_i == 1
+            raise Exception, "There appears to be a problem while running ExportPred, unexpected output form: \n#{error}"
+          end
+
+          # Error checking
+          unless [0,1].include?(result.length)
+            raise Exception, "Unexpected number of lines found in ExportPred output (#{result.length}:\n#{result}"
+          end
+
+          return Result.create_from_line(result[0])
+        end
+      end
+    end
+
+    class Result
+      @@all_result_names = [
+        :predicted,
+        :score
+      ]
+      @@all_result_names.each do |rn|
+        attr_accessor rn
+      end
+
+      # Given the STDOUT from the ExportPred program, create a programmatically manipulatable Bio::ExportPred::Result object
+      def self.create_from_line(line)
+        result = Result.new
+        if !line or line == '' #possible bug that scores below 2.3 don't work?
+          result.predicted = false
+          return result
+        end
+
+        # line is going to be something like
+        # metoo	RLE	6.44141	[a-met:M][a-leader:AVSTYNNTRRNGLRYVLKRR][a-hydrophobic:TILSVFAVICMLSL][a-spacer:NLSIFENNNNNYGFHCNKRH][a-RLE:FKSLAEA][a-tail:SPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETYKIPDEYKMRKFKFAHFEMQGYALKQEKFLLEYAFLSLNGKLCERKKFKEVLEYVKREWIEFRKSMFDVWKEKLASEFREHGEMLNQKRKLKQHELDRRAQREKMLEEHSRGIFAKGYLGEVESETIKKKTEHHENVNEDNVEKPKLQQHKVQPPKVQQQKVQPPKSQQQKVQPPKSQQQKVQPPKVQQQKVQPPKVQKPKLQNQKGQKQVSPKAKGNNQAKPTKGNKLKKN]
+        splits = line.split("\t")
+        raise Exception, "Badly parsed line: #{line}" if splits.length != 4
+        result.predicted = true
+        result.score = splits[2].to_f
+        return result
+      end
+
+      def predicted?
+        @predicted
+      end
+      alias_method :signal?, :predicted?
+
+      def self.all_result_names
+        @@all_result_names
+      end
+    end
+  end
+end

test/test_bio-exportpred.rb

@@ -1,7 +1,33 @@
 require 'helper'
 
 class TestBioExportpred < Test::Unit::TestCase
-  should "probably rename this file and start testing for real" do
-    flunk "hey buddy, you should probably rename this file and start testing for real"
+  def setup
+    @exportpred = Bio::ExportPred::Wrapper.new
+  end
+
+  def test_create_from_line
+    # test empty
+    line = ''
+    r = Bio::ExportPred::Result.create_from_line(line)
+    assert r
+    assert_kind_of Bio::ExportPred::Result, r
+    assert_equal false, r.predicted?
+
+    line = 'metoo	RLE	6.44141	[a-met:M][a-leader:AVSTYNNTRRNGLRYVLKRR][a-hydrophobic:TILSVFAVICMLSL][a-spacer:NLSIFENNNNNYGFHCNKRH][a-RLE:FKSLAEA][a-tail:SPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETYKIPDEYKMRKFKFAHFEMQGYALKQEKFLLEYAFLSLNGKLCERKKFKEVLEYVKREWIEFRKSMFDVWKEKLASEFREHGEMLNQKRKLKQHELDRRAQREKMLEEHSRGIFAKGYLGEVESETIKKKTEHHENVNEDNVEKPKLQQHKVQPPKVQQQKVQPPKSQQQKVQPPKSQQQKVQPPKVQQQKVQPPKVQKPKLQNQKGQKQVSPKAKGNNQAKPTKGNKLKKN]'
+    r = Bio::ExportPred::Result.create_from_line(line)
+    assert r
+    assert_kind_of Bio::ExportPred::Result, r
+    assert r.predicted?
+    assert_equal 6.44141, r.score
+  end
+
+  def test_wrapper_positive
+    positive = 'MAVSTYNNTRRNGLRYVLKRRTILSVFAVICMLSLNLSIFENNNNNYGFHCNKRHFKSLAEASPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETY'
+    assert_equal true, @exportpred.calculate(positive).signal?
+  end
+
+  def test_wrapper_negative
+    negative = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    assert_equal false, @exportpred.calculate(negative).signal?
   end
 end