bio-octopus 0.0.1 → 0.1.0

data/Rakefile

@@ -23,6 +23,9 @@ Jeweler::Tasks.new do |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'
+
+  #included so the IDE recognizes the file type of bin/biooctopus, but these are hard-linked so just use one of these two.
+  gem.files.exclude 'bin/biooctopus.rb' 
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.1.0

data/bin/biooctopus

@@ -5,14 +5,35 @@
 # Author:: Ben J Woodcroft
 # Copyright:: 2011
 # License:: The Ruby License
+require 'rubygems'
+require 'optparse'
+require 'bio'
+require 'bio-octopus'
 
- USAGE = "This scripts reads a fasta file in, and uses the BLOCTOPUS and SPOCTOPUS scripts, returning a structured result for each transmembrane domain. Requires the scripts to be installed before use. They are available from http://octopus.cbr.su.se/"
+USAGE = "This scripts reads a fasta file in, and uses the BLOCTOPUS and SPOCTOPUS scripts, returning a structured result for each transmembrane domain. Requires the scripts and a legacy BLAST formated database to be installed before use. They are available from http://octopus.cbr.su.se/"
 
 if $0 == __FILE__
+  o = OptionParser.new do |opts|
+    indent = '    '
+    opts.banner = [
+      "Usage: biooctopus <FASTA_FILE> <BLASTDB>\n",
+      USAGE
+    ].flatten
+  end
+  o.parse!
+  
+  unless ARGV.length == 2
+  	puts o.help
+  	exit
+  end
+  
+  fasta_path = ARGV[0]
+  blastdb_path = ARGV[1]
+
   runner = Bio::Spoctopus::Wrapper.new
 
-  Bio::FlatFile.auto(ARGF).each do |seq|
-    result = runner.calculate(seq.seq)
+  Bio::FlatFile.auto(File.open(fasta_path)).each do |seq|
+    result = runner.calculate(seq.seq, blastdb_path)
     name = seq.definition
 
     if result.has_domain?

data/bin/biooctopus.rb

@@ -0,0 +1,57 @@
+#!/usr/bin/env ruby
+#
+# BioRuby bio-octopus Plugin
+# Version 0.0.1
+# Author:: Ben J Woodcroft
+# Copyright:: 2011
+# License:: The Ruby License
+require 'rubygems'
+require 'optparse'
+require 'bio'
+require 'bio-octopus'
+
+USAGE = "This scripts reads a fasta file in, and uses the BLOCTOPUS and SPOCTOPUS scripts, returning a structured result for each transmembrane domain. Requires the scripts and a legacy BLAST formated database to be installed before use. They are available from http://octopus.cbr.su.se/"
+
+if $0 == __FILE__
+  o = OptionParser.new do |opts|
+    indent = '    '
+    opts.banner = [
+      "Usage: biooctopus <FASTA_FILE> <BLASTDB>\n",
+      USAGE
+    ].flatten
+  end
+  o.parse!
+  
+  unless ARGV.length == 2
+  	puts o.help
+  	exit
+  end
+  
+  fasta_path = ARGV[0]
+  blastdb_path = ARGV[1]
+
+  runner = Bio::Spoctopus::Wrapper.new
+
+  Bio::FlatFile.auto(File.open(fasta_path)).each do |seq|
+    result = runner.calculate(seq.seq, blastdb_path)
+    name = seq.definition
+
+    if result.has_domain?
+      # At least one TMD found. Output each on a separate line
+      result.transmembrane_domains.each do |tmd|
+        puts [
+          name,
+          result.transmembrane_type,
+          tmd.start,
+          tmd.stop,
+          tmd.orientation
+        ].join("\t")
+      end
+    else
+      puts [
+        name,
+        'No Transmembrane Domain Found'
+      ].join("\t")
+    end
+  end
+end

data/bio-octopus.gemspec

@@ -5,15 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-octopus}
-  s.version = "0.0.1"
+  s.version = "0.1.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ben J Woodcroft"]
-  s.date = %q{2011-04-10}
-  s.default_executable = %q{biooctopus}
+  s.date = %q{2011-04-17}
   s.description = %q{Running and parsing of the protein transmembrane domain predictor octopus}
   s.email = %q{gmail.com after donttrustben}
-  s.executables = ["biooctopus"]
+  s.executables = ["biooctopus.rb", "biooctopus"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -29,6 +28,10 @@ Gem::Specification.new do |s|
     "bio-octopus.gemspec",
     "lib/bio-octopus.rb",
     "lib/bio/appl/octopus.rb",
+    "test/data/dummyLegacyDb",
+    "test/data/dummyLegacyDb.phr",
+    "test/data/dummyLegacyDb.pin",
+    "test/data/dummyLegacyDb.psq",
     "test/helper.rb",
     "test/test_bio-octopus.rb"
   ]

data/lib/bio/appl/octopus.rb

@@ -1,16 +1,24 @@
 require 'fastercsv'
 require 'bio-tm_hmm'
+require 'rio'
 
 module Bio
   class Spoctopus
     class Wrapper
       TMP_SEQUENCE_NAME = 'wrapperSeq'
+      BLOCTOPUS_DEFAULT_PATH='BLOCTOPUS.sh'
+      SPOCTOPUS_DEFAULT_PATH='SPOCTOPUS.sh'
+      
+      # The path to the BLOCTOPUS executable, by default BLOCTOPUS_DEFAULT_PATH
+      attr_accessor :bloctopus_executable
+      
+      # The path to the SPOCTOPUS executable, by default SPOCTOPUS_DEFAULT_PATH
+      attr_accessor :spoctopus_executable
 
       def calculate(sequence, blast_database_path)
         # Remove stop codons, as these mess things up for the predictor
         sequence.gsub!('*','')
 
-
         rio(:tempdir) do |d| # Do all the work in a temporary directory
           FileUtils.cd(d.to_s) do
           
@@ -36,9 +44,10 @@ module Bio
             # ben@ben:~/bioinfo/spoctopus$ ./BLOCTOPUS.sh /tmp/spoctopus/names /tmp/spoctopus/fa
             # /tmp/spoctopus/tmd blastall blastpgp`
             # /blastdb/UniProt15/uniprot_sprot.fasta makemat -P
+            # 
             Tempfile.open('octopuserr') do |err|
               result = system [
-                'BLOCTOPUS.sh',
+                @bloctopus_executable.nil? ? BLOCTOPUS_DEFAULT_PATH : @bloctopus_executable,
                 "#{Dir.pwd}/names",
                 "#{Dir.pwd}/fasta",
                 "#{Dir.pwd}/tmd",
@@ -47,12 +56,12 @@ module Bio
                 "'#{blast_database_path}'",
                 'makemat',
                 '-P',
-                '>/dev/null' # SPOCTOPUS doesn't understand the concept of STDERR
-                #                "2>#{err.path}"
+                '>/dev/null', # SPOCTOPUS doesn't understand the concept of STDERR
+                "2>#{err.path}"
               ].join(' ')
 
               if !result
-                raise Exception, "Running BLOCTOPUS program failed. $? was #{$?.inspect}. STDERR was #{err.read}"
+                raise Exception, "Running BLOCTOPUS program failed. $? was #{$?.inspect}. Has it been installed properly? STDERR: #{File.open(err.path).read}"
               end
             end
 
@@ -64,17 +73,17 @@ module Bio
             # /tmp/spoctopus/tmd/
             Tempfile.open('octopuserr') do |err|
               result = system [
-                'SPOCTOPUS.sh',
+                @spoctopus_executable.nil? ? SPOCTOPUS_DEFAULT_PATH : @soctopus_executable,
                 "#{Dir.pwd}/names",
                 "#{Dir.pwd}/tmd/PSSM_PRF_FILES/",
                 "#{Dir.pwd}/tmd/RAW_PRF_FILES/",
                 "#{Dir.pwd}/tmd/",
-                '>/dev/null' # SPOCTOPUS doesn't understand the concept of STDERR
-                #                "2>#{err.path}"
+                '>/dev/null', # SPOCTOPUS doesn't understand the concept of STDERR
+                "2>#{err.path}"
               ].join(' ')
 
               if !result
-                raise Exception, "Running SPOCTOPUS program failed. $? was #{$?.inspect}. STDERR was #{err.read}"
+                raise Exception, "Running SPOCTOPUS program failed. $? was #{$?.inspect}. Has it been installed properly? STDERR: #{File.open(err.path).read}"
               end
             end
             
@@ -109,7 +118,7 @@ module Bio
         
         # Error checking
         unless lines[0].match(/^\>/) and lines.length > 1
-          raise Exception, "Unexpected SPOCTOPUS output file: #{spoctopus_output.inspect}"
+          raise Exception, "Unexpected OCTOPUS output file: #{spoctopus_output.inspect}. STDERR: #{File.open(err.path).read}"
         end
 
         seq = lines[1..(lines.length-1)].join('')
@@ -173,57 +182,5 @@ module Bio
         return tmd
       end
     end
-
-    # Read the output from this file when it is run as a script and return
-    # useful programmatic objects - TransmembraneProteins
-    #
-    #pfa|PFD0635c	I	1833	1853	outside_in
-    #pfa|PFD0595c	I	2	22	outside_in
-    #pfa|PFB0610c	No Transmembrane Domain Found
-    #pfa|PFF1525c	Unknown	2	22	outside_in
-    #pfa|PFF1525c	Unknown	160	180	inside_out
-    #pfa|PFF1525c	Unknown	188	208	outside_in
-    class WrapperParser
-      attr_accessor :io
-
-      def initialize(io)
-        @io = io
-      end
-
-      # Return an array of transmembrane proteins
-      def transmembrane_proteins
-        transmembrane_proteins = []
-        current_transmembrane_protein = nil
-
-        FasterCSV.foreach(@io, :col_sep => "\t") do |row|
-          next if row.length == 0
-          current_protein_id = row[0]
-          
-          # if the protein ID changes then return the last protein 
-          # (if there is one)
-          unless current_transmembrane_protein.nil? or
-              current_transmembrane_protein.name == current_protein_id
-            transmembrane_proteins.push current_transmembrane_protein
-            current_transmembrane_protein = nil
-          end
-
-          # deal with no tmd proteins
-          if row[1] == 'No Transmembrane Domain Found'
-            prot = Bio::Transmembrane::OrientedTransmembraneDomainProtein.new
-            prot.name = current_protein_id
-            transmembrane_proteins.push prot
-            current_transmembrane_protein = nil
-          else
-            current_transmembrane_protein ||= Bio::Transmembrane::OrientedTransmembraneDomainProtein.new
-            current_transmembrane_protein.name = current_protein_id
-            current_transmembrane_protein.transmembrane_domains.push Bio::Transmembrane::OrientedTransmembraneDomain.new(row[2],row[3],row[4])
-          end
-        end
-        # push the last one
-        transmembrane_proteins.push current_transmembrane_protein unless current_transmembrane_protein.nil?
-
-        return transmembrane_proteins
-      end
-    end
   end
 end

data/test/data/dummyLegacyDb

@@ -0,0 +1,49 @@
+>PB000746.03.0 chloroquine resistance transporter, putative
+FKIIGNEMKNNVYVYLLSILYLCVCVMNKVFAKRTLNKMGNYSFVTSETHNIICIIVFQLLYFIYRKTSSSSVYKNESQK
+NFGWQFFLISLLDASTVIISMIGLTRTTGNIQSFIMQLIIPVNMYFCFMFLGYRYHLFNYLGAFIILITIAVVETFLSFE
+TQGENSIIFNLIMISALIPLSFSNMTREVVFKKHKINILRLNAMVVLFQFFTSLLVLPVYNIPFLKEIYMPFSEMSTNIN
+NGLRCLFYGENTIVENCGVGMVKMCDNCEGAWKTFITFSFFNICDNLLACYIIDKFSTMTYTIVSCIQGPAITIAYYFKF
+LAGDAVRKPRILDFLTLFGYLFGTIIYRIGNIILEKKQVIKSQNSNDSEAELTSIETSRA
+>cgd6_4890 transporter protein with conserved Zn ribbon C11C7CxxC
+MNGSGRELLLGSESENEQIQIITLIKNGMSALNEGVIKPCKENFFLIVCMMSLLISSVFNSVFFKKMTSAMPNHVWFLTQ
+LTSALYIPLFGLVLLISYFRGELSRDNLEFPMSKFWMMGFFDAFSSILTLLASTHTSGVMQVVLGQMCTPITLVMLSSIC
+KDRFHKLQYIGATVMVMGIFIVKSTLILGIRKSSGAENSNQLIFNILFVIACIPASASSVYKDLSFREYSSLNENYLQFC
+VAATQVIIGFILVPINSLSILGPQKIEMNQIPSLLFDGANCLFLKRNSITESCGGELQRPCDNCNSAQFPVLIYFIANVI
+CNVFSVLVLKHGTASTGFIVSTLRLPVTTLVFFSPRLVGKEATEPKVEDLIGILILILGLILYRLGSVKINQEEEEIQTE
+EEPERDYYELSSMTYSKETIDKIKSNTSSTTCSFNIEYDSSHFHSS
+>PCAS_122020 chloroquine resistance transporter, putative
+MTGMKKGKNKKKNVKNDERYKELDSLISNDSEIGNNSRWGGAKRICKLIGNEMRNNIYVYLLSILYLCVSVMNKVFSKRT
+LNKIGNYSFVTSEVHNMICTIVFQLLYFIYRKTSNPASRNESQKNFGWQFFLISLLDASTVIITMIGLTRTTGNIQSFIM
+QLIIPVNMYFCFIFLGYRYHLFNYLGAFIILITIAAVETVLSYETQSDNSIIFNLIMIFALIPLSFSNMTREVVFKKHKI
+NIIRLNAMVALFQFFTSLLVLPVYNISFLKEIYMPFSEMGTNINDGLRCLFYGQSTIVENCGVGMVKMCDQCEGAWKTFI
+TYSFFNICDNLLVCYIIDKFSTMTYTIVSCIQGPAITIAYYFKFLAGDVVRQPRLLDFLTLFGYLLGTIIYRIGNIILEK
+KKMLKAQNTDGSEAELTSIETSTA
+>TA12005 transporter protein cg10, putative
+MLKEGSSLDLSASSSSGTLRSDNSFGNSPLDRITSLLILIYKSIRACFKWIYSKSFGIICILFVILDVLTTVFFKRFIDH
+TKNYVMFTIQVIIFTFWIIVCCIAILCFLFNREYMKRHFNVRPLVFLGFLDMLSTGLSANGSAHTSGLMLVLLGQISVPL
+TMVSCKLILSKKYHHYQYISSAIILTFAVLKPILNRTDTTDNRFYNNMLYLLASVPDSIASALREKQYTSKFFHVVKYQF
+FGFLFHFFYNILYTLLFTLPFNSVKGYFDSLYKLCVNGYKCIFFGVNTITENCGPTLIPTCDNCLEAFKIYCLYILFSSA
+IRVAYVFIMLDGSVTFTLLLGTVKVPLTSIAFSLRFIAGDSTTSFNLLDVVCFLGIVAGLLLYALGSKKIQEETDLLESP
+LIDDAESEHELLSTGTEKLMRSEICHDLFT
+>PY05061 putative transporter protein CG10
+MTVIKKGKNKKKNLKNDDRYKELDSLITNGSEIGDNSGRSCIKRFFKIIGNEMKNNVYVYFLSILYLCVCVMNKVFAKRT
+LNKMGNYSFVTSETHNIICIVVFQLLYFIYRKTSTSGYKNESQKNFGWQFFLISLLDASTVIISMIGLTRTTGNIQSFIM
+QLIIPVNMYFCFMFLGYRYHLFNYLGAFIILITIAVVETFLSFETQSENSIIFNLIMISALIPLSFSNMTREVVFKKHKI
+NILRLNAMVVLFQFFTSLLVLPVYNIPFLKEIYMPFSEMSTNINNGLRCLFYGQNTVVENCGVGMVKMCDNCEGAWKTFI
+TFSFFNICDNLLACYIIDKFSTMTYTIVSCIQGPAITIAYYFKFLAGDAVRKPRILDFLTLFGYLFGTIIYRIGNIILEK
+KKMVKSQNSNDSEAELTCIETSTA
+>PVX_087980 chloroquine resistance transporter, putative
+MTILKKKKKGSPQITPDERYRELDSHAQNESEIQEDVPISRKIANFLKLAYNEIRENISIYLLIIVYLCVCVMNKLLAKR
+TLKKIGNYSFVTSETHNCICMVVFFALYFMFGRRVMSAKERHRNFGVQFLLISLLDACSVIIAFIGLTRTTGNIQSFVMQ
+LSIPINMFFCFLILRYRYHLFNYVGAFIIVVTIAVVEFMLSFETQEENSIVFNLVLIASLIPLSFSNMTREIVFKKYKIN
+ILRLNAVVSFFQIFTSCLMLPMYTLPFLKQINLPFSEIGTNIKNGFRCLFLGQNTIVENCGLGMSKMCDDCEGAWKTFIA
+YSFFNICDNLITSFIIEKFSTMTYTIVSCIQGPAIAIAYYFKFLAGDAVMQPRMLDFVTLFGYLFGSIIYRIGNIILEKK
+RMMEAGNDDDSEGELTNADSIITH
+>TGME49_113930 hypothetical protein, conserved
+MPNYSPCLTQVTTVVFVPVFFALSLYTDYAGGLPQEMADFPKRNFAVMGFLDSFSGVMAIIGAVHTTGTTQVVLQQSCIV
+FSLLASIVMLRKRFHAAHYLGALVIILGVLVVKLPDLLHPSSDGGGDVFVFNLLYLLSNLPTAVSCVYKEVAFRGVEMGT
+NYLQAWVALFQFLIGFLVLPLNALPVLGPQRVPLAELPASLWNGTRCLFGFNTIVTNCGGAGNMESPCDNCEGAWKYVGM
+YLSFNLLYNMFIIFVVKSGGAALTFLVSTLRLPVTALAFCSRAIMGDRAVPPKATDFYGLLVLILGLVIYRAGGIMKRRA
+QRRAVAAARGHTSSPMMLTPREEEQIGTIFVEEVFAAGELEDGGVTEEDETDDDTSEVEVHPVFSSVVASEPPHVYVHTK
+RHSHSDGGYHKLPACGSSPAAFTPFTQRMPGTGSESCSRRRNRDGDDERSPRSHACSFDEETGFAGGTGTGRHFSSPGTA
+LSPNRVGGYEPPSMHAVQPAVIGKSRANNGCI

data/test/test_bio-octopus.rb

@@ -1,8 +1,9 @@
 require 'helper'
 require 'tempfile'
-require 'bio-tm_hmm'
 
 class TestBioOctopus < Test::Unit::TestCase
+	DATA_DIR = File.join(Dir.pwd,'test','data')
+	 
   def test_no_tmd_result
     res = Bio::Spoctopus::Result.create_from_output([
         '>wrapperSeq',
@@ -81,58 +82,23 @@ iiiiiiiiiMMMMMMMMMMMMMMMMMMMMMooooo'
     assert_equal false, res.signal?
     assert res.has_domain?
   end
-
-  def test_wrapper_read
-    Tempfile.open('spock') do |tempfile|
-      tempfile.puts ''
-      tempfile.flush
-
-      pees = Bio::Spoctopus::WrapperParser.new(tempfile.path).transmembrane_proteins
-      assert_equal [], pees
-    end
-
-    Tempfile.open('spock') do |tempfile|
-      tempfile.puts 'pfa|PFD0635c	I	1833	1853	outside_in'
-      tempfile.flush
-
-      pees = Bio::Spoctopus::WrapperParser.new(tempfile.path).transmembrane_proteins
-      assert_equal 1, pees.length
-      r = pees[0]
-      assert_equal 'pfa|PFD0635c', r.name
-      assert_equal 1, r.transmembrane_domains.length
-      t = r.transmembrane_domains[0]
-      assert_equal 1833, t.start
-      assert_equal 1853, t.stop
-      assert r.transmembrane_type_1?
-    end
-
-    Tempfile.open('spock') do |tempfile|
-      tempfile.puts 'pfa|PFD0635c	I	1833	1853	outside_in
-pfa|PFD0595c	II	2	22	inside_out
-pfa|PFB0610c	No Transmembrane Domain Found
-pfa|PFF1525c	Unknown	2	22	outside_in
-pfa|PFF1525c	Unknown	160	180	inside_out
-pfa|PFF1525c	Unknown	188	208	outside_in'
-      tempfile.flush
-
-      pees = Bio::Spoctopus::WrapperParser.new(tempfile.path).transmembrane_proteins
-      assert_equal 4, pees.length
-      r = pees[0]
-      assert_equal 'pfa|PFD0635c', r.name
-      assert_equal 1, r.transmembrane_domains.length
-      t = r.transmembrane_domains[0]
-      assert_equal 1833, t.start
-      assert_equal 1853, t.stop
-      assert r.transmembrane_type_1?
-
-      r = pees[1]
-
-      assert r.transmembrane_type_2?
-
-      assert_equal 'pfa|PFB0610c', pees[2].name
-      assert_equal false, pees[2].has_domain?
-
-      assert_equal 3, pees[3].transmembrane_domains.length
-    end
+  
+  def test_wrapper_by_actually_running_the_underlying_program
+  	sequence = "MKFASKKNNQKNSSKNDERYRELDNLVQEGNGSRLGGGSCLGKCAHVFKLIFKEIKDNIFIYILSIIYLSVCVMNKIFAK
+RTLNKIGNYSFVTSETHNFICMIMFFIVYSLFGNKKGNSKERHRSFNLQFFAISMLDACSVILAFIGLTRTTGNIQSFVL
+QLSIPINMFFCFLILRYRYHLYNYLGAVIIVVTIALVEMKLSFETQEENSIIFNLVLISALIPVCFSNMTREIVFKKYKI
+DILRLNAMVSFFQLFTSCLILPVYTLPFLKQLHLPYNEIWTNIKNGFACLFLGRNTVVENCGLGMAKLCDDCDGAWKTFA
+LFSFFNICDNLITSYIIDKFSTMTYTIVSCIQGPAIAIAYYFKFLAGDVVREPRLLDFVTLFGYLFGSIIYRVGNIILER
+KKMRNEENEDSEGELTNVDSIITQ".gsub(/\n/,'') #this is PfCRT, MAL7P1.27
+		Tempfile.open('pfcrt') do |tempfile|
+			tempfile.puts sequence
+			tempfile.close
+			
+			blastdb_path =  File.join(DATA_DIR,'dummyLegacyDb')
+  		result = Bio::Spoctopus::Wrapper.new.calculate(sequence, blastdb_path)
+			assert_kind_of Bio::Transmembrane::SignalPeptideTransmembraneDomainProtein, result
+			assert_equal false, result.signal?
+			assert_equal 58, result.transmembrane_domains[0].start
+		end
   end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: bio-octopus
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 27
   prerelease: 
   segments: 
   - 0
-  - 0
   - 1
-  version: 0.0.1
+  - 0
+  version: 0.1.0
 platform: ruby
 authors: 
 - Ben J Woodcroft
@@ -15,8 +15,8 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-10 00:00:00 +10:00
-default_executable: biooctopus
+date: 2011-04-17 00:00:00 +10:00
+default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   type: :runtime
@@ -141,6 +141,7 @@ dependencies:
 description: Running and parsing of the protein transmembrane domain predictor octopus
 email: gmail.com after donttrustben
 executables: 
+- biooctopus.rb
 - biooctopus
 extensions: []
 
@@ -158,8 +159,13 @@ files:
 - bio-octopus.gemspec
 - lib/bio-octopus.rb
 - lib/bio/appl/octopus.rb
+- test/data/dummyLegacyDb
+- test/data/dummyLegacyDb.phr
+- test/data/dummyLegacyDb.pin
+- test/data/dummyLegacyDb.psq
 - test/helper.rb
 - test/test_bio-octopus.rb
+- bin/biooctopus.rb
 has_rdoc: true
 homepage: http://github.com/wwood/bioruby-octopus
 licenses: