scbi_go 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 83904a2d1485297ab2d08126daf42483ef2c0ed4
+  data.tar.gz: 860216b0165531eec340e9899bd491b129125813
+SHA512:
+  metadata.gz: 082e8c723d017e82c631044455b9624864c3ea409841da476de9db94b789610dad4eb2b3e0ddcb1fe0559b7f3eb7f7e711e8e3e93fe89ebd7f79c4c5d05db018
+  data.tar.gz: 71812aeb8eac6e72485c681ebcc94a2eab2c0843640f51a850ad2130bba48ef8e4c537e0a50e26e7f1fee195eccf6b56384080174859dc10a8090530ac2b2b58

data/.autotest

@@ -0,0 +1 @@
+require "autotest/bundler"

data/.gitignore

@@ -0,0 +1,14 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in scbi_go.gemspec
+gemspec

data/Guardfile

@@ -0,0 +1,32 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+## Uncomment and set this to only include directories you want to watch
+# directories %w(app lib config test spec features) \
+#  .select{|d| Dir.exists?(d) ? d : UI.warning("Directory #{d} does not exist")}
+
+## Note: if you are using the `directories` clause above and you are not
+## watching the project directory ('.'), then you will want to move
+## the Guardfile to a watched dir and symlink it back, e.g.
+#
+#  $ mkdir config
+#  $ mv Guardfile config/
+#  $ ln -s config/Guardfile .
+#
+# and, you'll have to watch "config/Guardfile" instead of "Guardfile"
+
+# Note: The cmd option is now required due to the increasing number of ways
+#       rspec may be run, below are examples of the most common uses.
+#  * bundler: 'bundle exec rspec'
+#  * bundler binstubs: 'bin/rspec'
+#  * spring: 'bin/rspec' (This will use spring if running and you have
+#                          installed the spring binstubs per the docs)
+#  * zeus: 'zeus rspec' (requires the server to be started separately)
+#  * 'just' rspec: 'rspec'
+
+guard :rspec, cmd: "bundle exec rspec" do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/(.+)\.rb$})     { |m| "spec/lib/#{m[1]}_spec.rb" }
+  watch(%r{^lib/.*/(.+)\.rb$})     { |m| "spec/lib/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+end

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2015 dariogf
+
+MIT License
+
+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.md

@@ -0,0 +1,31 @@
+# ScbiGo
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'scbi_go'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install scbi_go
+
+## Usage
+
+See spec files to usage examples
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/scbi_go/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

@@ -0,0 +1,8 @@
+require "bundler/gem_tasks"
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new
+
+task :default => :spec
+task :test => :spec
+

data/lib/scbi_go/ancestors_graph.rb

@@ -0,0 +1,25 @@
+module ScbiGo
+  class AncestorsGraph < BaseGraph
+
+    # override the way that nodes are painted in dot
+  	def build_dot_lines(nodes)
+
+		res =[]
+		res << "digraph #{@graph_name} {"
+		nodes.each do |node|
+			res << "#{node.id.gsub(':','_')}[label=\"#{node.id}\n#{node.name}\"];"
+		end
+
+		nodes.each do |node| 
+
+			node.is_a.each do |parent|
+				res << "#{parent.id.gsub(':','_')} -> #{node.id.gsub(':','_')} ;"
+			end
+		end
+
+		res << "}"
+		return res
+  	end
+
+  end
+end

data/lib/scbi_go/base_graph.rb

@@ -0,0 +1,37 @@
+module ScbiGo
+  class BaseGraph
+
+    #create a dot file and optional pdf file
+  	def initialize(nodes, file_name=nil, name='my_graph', generate_pdf=false)
+      @graph_name=name
+
+      if !nodes.empty?
+        res =[]
+        res += build_dot_lines(nodes)
+        if !file_name.nil?
+          f=File.new(file_name,'w')
+          f.puts res
+          f.close
+
+        if generate_pdf
+          system("dot -Tpdf #{file_name} -o #{file_name}.pdf")
+        end
+
+        end
+      end 
+    end
+  	
+    # define the way that nodes are painted in dot
+    def build_dot_lines(nodes)
+
+      res =[]
+      res << "graph #{@graph_name} {"
+        nodes.each do |node|
+          res << "#{node.id.gsub(':','_')}[label=\"#{node.id}\n#{node.name}\"];"
+        end
+      res << "}"
+      return res
+    end
+
+  end
+end

data/lib/scbi_go/descendants_graph.rb

@@ -0,0 +1,24 @@
+module ScbiGo
+  class DescendantsGraph < BaseGraph
+
+    # override the way that nodes are painted in dot
+  	def build_dot_lines(nodes)
+  		res = []
+		res << "digraph #{@graph_name} {"
+
+  		nodes.each do |node|
+  			res << "#{node.id.gsub(':','_')}[label=\"#{node.id}\n#{node.name}\"];"
+  		end
+  		nodes.each do |node| 
+  			node.children.each do |child|
+  				res << "#{node.id.gsub(':','_')} -> #{child.id.gsub(':','_')} ;"
+  			end
+  		end
+  		
+  		res << "}"
+
+	  	return res
+  	end
+
+  end
+end

data/lib/scbi_go/gene_ontology.rb

@@ -0,0 +1,104 @@
+require 'zlib'
+
+module ScbiGo
+  class GeneOntology
+
+  	attr_accessor :gos, :header, :base_terms
+  	
+    # load a new gene ontology fiel in obo format, in gz or un-gzipped format
+  	def initialize(filename='lib/data/go.obo.gz')
+
+      if !File.exists?(filename)
+        raise "File does not exists: #{filename}"
+      end
+      #t1=Time.now
+      @filename=filename
+      begin
+        my_obo_file=Zlib::GzipReader.open(filename)
+      rescue Zlib::GzipFile::Error # not in gzip file
+        my_obo_file=File.open(@filename) # open as normal file
+      end
+
+      
+      #@cache_filename='/dev/shm/'+File.basename(@filename)+'.dump'
+      @base_terms=[]
+      @gos={}
+      @header=nil
+
+      # if File.exists?(@cache_filename)
+      #   puts "using cache: #{@cache_filename}"
+      #   o=Marshal.load(File.new(@cache_filename))
+        
+      #   @base_terms=o.base_terms
+      #   @gos=o.gos
+      #   @header=o.header
+
+      # else
+
+    		# Parse Obo data file with external lib
+    		obo = Obo::Parser.new(filename)
+    		go_list = obo.elements(my_obo_file).to_a
+    		obo=nil
+
+    		#first element is header
+    		@header = ScbiGo::Header.new(go_list.shift)
+
+    		# other elements are go terms
+    		go_list.each do |go_term|
+    			add_go_term(go_term)
+    		end
+
+        add_children_relations
+
+        go_list=nil
+
+        #save cache file
+      #   Marshal.dump(self, File.new(@cache_filename,'w'))
+      # end
+      #puts "Load time #{Time.now-t1} seg"
+  	end
+
+  	# find a go_term by it name
+  	def find_go(go_id)
+  		@gos[go_id]
+  	end
+
+    # add new term
+  	def add_go_term(go_term)
+  		if go_term.name =='Term' && go_term['is_obsolete'].nil?
+	  		new_term=ScbiGo::GoTerm.new(go_term, self)
+	  		@gos[go_term['id']] = new_term
+	  		if new_term.base_term?
+	  			@base_terms<<new_term
+	  		end
+  		end
+  	end
+
+    #convert a list of go names to terms, ignore not found gos
+    def go_list_to_terms(go_list)
+      res=[]
+
+      go_list.each do |s|
+        if s.is_a?(GoTerm)
+          res << s
+        else
+          res << find_go(s)
+        end
+      end
+
+      return res.compact
+    end
+
+private
+
+    # add children links to parents once Go file is loaded
+  	def add_children_relations
+  		@gos.each do |go_id, go|
+  			go.is_a.each do |parent|
+  					parent.add_child(go)
+  			end
+  		end
+  	end
+  	
+  end
+end

data/lib/scbi_go/go_list_reducer.rb

@@ -0,0 +1,90 @@
+module ScbiGo
+  class GoListReducer < GeneOntology
+
+
+    # return the subset of branches not contained in another branch of the list
+    def simplify_branches(branches)
+      res=[]
+
+      # inverse sort branches by length
+      sorted_b = branches.sort{|b1,b2| -b1.length<=>-b2.length}
+
+      # simplify by iteration from larger to smaller
+
+      sorted_b.each do |branch|
+        # select other branches in res that contains all elements of this branch
+        matches=res.select{|e| (e & branch).length==branch.length}
+
+        # add it to res if no match found
+        if matches.empty?
+          res << branch
+        end
+      end
+      
+      return res
+    end
+
+
+    # given a go_list, returns the leaves of all the branches defined by them
+    def reduce_branches(go_list)
+      terms = go_list_to_terms(go_list)
+      
+      res=[]
+      branches=[]
+
+      if !terms.empty?
+        #get all branches for each terms
+        terms.each do |term|
+         branches += term.all_branches_to_top
+        end
+        
+        branches=simplify_branches(branches)
+
+        #return first unique element of each branch
+        res=branches.map{|b| b.first}.uniq
+      end
+
+      return res
+    end
+
+    # return all branches that match with the elements of go_list
+    # is the same as reduce_branches, but returning whole branches
+  	def all_matching_branches(go_list)
+        leaves = reduce_branches(go_list)
+        res=[]
+
+        leaves.each do |leave|
+          res += leave.all_branches_to_top
+        end
+
+    		return simplify_branches(res)
+    end
+
+    # get the branch/es that match more elements in the go_list
+    def best_matching_branches(go_list)
+        matching_count = {}
+
+        terms=go_list_to_terms(go_list)
+
+        leaves = reduce_branches(go_list)
+
+        branches = leaves.first.all_branches_to_top
+
+        branches.each do |branch|
+          intersect_count = (branch & terms).count
+
+          if intersect_count>0
+            matching_count[intersect_count] = [] if matching_count[intersect_count].nil?
+            matching_count[intersect_count] << branch
+          end
+        end
+
+        res = []
+        if m=matching_count.keys.max
+          res = matching_count[m]
+        end
+
+        return res
+    end
+  end
+end

data/lib/scbi_go/go_term.rb

@@ -0,0 +1,113 @@
+module ScbiGo
+  class GoTerm
+  	attr_accessor :id, :name, :def, :namespace, :subset, :comment, :consider, :synonym
+
+  	def initialize(go_term, gene_ontology)
+
+  		@term_type=go_term.name
+  		@gene_ontology=gene_ontology
+  		@id=go_term['id']
+  		@name=go_term['name']
+  		@def=go_term['def']
+  		@namespace=go_term['namespace']
+
+      #to save is_a relation as strings, cannot save objects directly because they may be not loaded yet.
+      @is_a_str=[]
+      # tmp var to save a cache with is_a relation as objects
+  		@is_a=nil
+  		if go_term['is_a'].is_a?(Array)
+  			@is_a_str=go_term['is_a']
+  		elsif !go_term['is_a'].nil?
+  			@is_a_str=[go_term['is_a']]
+  		end
+
+  		@subset=go_term['subset']
+  		@comment=go_term['comment']
+  		@consider=go_term['consider']
+  		@synonym=go_term['synonym']
+		  @children = []
+  	end
+
+    #base terms have no parents
+    def base_term?
+      return @is_a_str.count==0
+    end
+
+    def is_a
+      convert_is_a_to_terms! if @is_a.nil?
+      @is_a
+    end
+
+    # add another node ad child
+  	def add_child(child)
+  		@children << child
+  	end
+
+  	def inspect
+  		"#{@term_type}:#{@id}, #{@name}, is_a: #{@is_a}"
+  	end
+
+    def parents
+      is_a
+    end
+
+    def children
+      @children
+    end
+
+
+  	# get list of descendants for a node
+  	def descendants
+  		res=children
+  		children.each {|c| res += c.descendants}
+  		return res.uniq
+  	end
+
+    # include myself in descendants
+    def self_and_descendants
+      res = [self] + self.descendants
+      return res.uniq
+    end
+
+    # get list of ancestors for a node
+  	def ancestors 
+  		res=parents
+  		parents.each {|c| res += c.ancestors}
+  		return res.uniq
+  	end
+
+    # include myself in ancestors
+  	def self_and_ancestors
+  		res = [self] + self.ancestors
+  		return res.uniq
+  	end
+
+    # recursive function to get all branches from myself to top of the ontology
+    def all_branches_to_top
+
+      res=[]
+      if parents.count == 0
+        res = [[self]]
+      else
+        parents.each do |parent|
+            parent_b = parent.all_branches_to_top
+            parent_b.each do |pb|
+              res << pb.unshift(self)
+            end
+        end
+      end
+
+      return res
+
+    end
+
+  private
+
+    # cache is_a terms
+    def convert_is_a_to_terms!
+       @is_a = @is_a_str.map { |ia| @gene_ontology.find_go(ia) }
+    end
+
+
+  end
+end

data/lib/scbi_go/header.rb

@@ -0,0 +1,15 @@
+module ScbiGo
+	
+  class Header
+  	attr_accessor :format_version
+
+  	def initialize(header)
+  		@format_version=header['format-version']
+  	end
+
+  	def inspect
+  		puts "GO HEADER: #{@format_version}"
+  	end
+
+  end
+end

data/lib/scbi_go/version.rb

@@ -0,0 +1,3 @@
+module ScbiGo
+  VERSION = "0.0.1"
+end

data/lib/scbi_go.rb

@@ -0,0 +1,15 @@
+require "scbi_go/version"
+require 'obo'
+require 'json'
+require 'scbi_go/header'
+require 'scbi_go/base_graph'
+require 'scbi_go/ancestors_graph'
+require 'scbi_go/descendants_graph'
+require 'scbi_go/go_term'
+require 'scbi_go/gene_ontology'
+require 'scbi_go/go_list_reducer'
+
+
+module ScbiGo
+
+end

data/scbi_go.gemspec

@@ -0,0 +1,30 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'scbi_go/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "scbi_go"
+  spec.version       = ScbiGo::VERSION
+  spec.authors       = ["dariogf"]
+  spec.email         = ["dariogf@gmail.com"]
+  spec.summary       = %q{GeneOntology tools.}
+  spec.description   = %q{GeneOntology tools to summarize and graph go terms}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec"
+  #spec.add_development_dependency "autotest"
+  spec.add_development_dependency "guard-rspec"
+  
+  spec.add_runtime_dependency "obo"
+  
+  #spec.add_runtime_dependency "gene_ontology"
+end

data/spec/lib/ancestors_graph_spec.rb

@@ -0,0 +1,20 @@
+require 'spec_helper'
+
+describe ScbiGo::AncestorsGraph do
+	before(:all) do
+    	@go=ScbiGo::GeneOntology.new
+   
+  	end
+	
+	it "Should make a graph and dot file" do
+		g=@go.find_go('GO:0001071');
+		g=@go.find_go('GO:0031323')
+		file_name="/tmp/dot_#{Time.now.strftime('%s')}.dot"
+		@graph=ScbiGo::AncestorsGraph.new(g.self_and_ancestors,file_name,'grafica',true)
+		expect(File).to exist(file_name)
+		expect(File).to exist(file_name+'.pdf')
+		
+	end
+
+
+end

data/spec/lib/base_graph_spec.rb

@@ -0,0 +1,21 @@
+require 'spec_helper'
+
+describe ScbiGo::BaseGraph do
+	before(:all) do
+    	@go=ScbiGo::GeneOntology.new
+  	end
+
+	it "Should make graph and dot file" do
+		g1=@go.find_go('GO:0001071');
+		g2=@go.find_go('GO:0001074');
+		
+		file_name="/tmp/dot_#{Time.now.strftime('%s')}.dot"
+
+		@graph=ScbiGo::BaseGraph.new([g1,g2],file_name,'grafica',true)
+		expect(File).to exist(file_name)
+		expect(File).to exist(file_name+'.pdf')
+		
+	end
+
+
+end

data/spec/lib/descendants_graph_spec.rb

@@ -0,0 +1,18 @@
+require 'spec_helper'
+
+describe ScbiGo::DescendantsGraph do
+	before(:all) do
+    	@go=ScbiGo::GeneOntology.new
+   
+  	end
+	
+	it "Should make a graph and dot file" do
+		g=@go.find_go('GO:0001071');
+		file_name="/tmp/dot_#{Time.now.strftime('%s')}.dot"
+		@graph=ScbiGo::DescendantsGraph.new(g.self_and_descendants,file_name,'grafica',true)
+		expect(File).to exist(file_name)
+		expect(File).to exist(file_name+'.pdf')
+		
+	end
+
+end

data/spec/lib/gene_ontology_spec.rb

@@ -0,0 +1,63 @@
+require 'spec_helper'
+
+describe ScbiGo::GeneOntology do
+	before(:all) do
+    	@go=ScbiGo::GeneOntology.new
+  	end
+
+
+	it "Should load obo file version 1.2" do
+		expect(@go.header.format_version).to eq('1.2')
+	end
+
+	it "Should have 41250 Go terms loaded" do
+		expect(@go.gos.count).to be 41250
+	end
+
+	it "Should find a go term object by a name string" do
+		go_term = @go.find_go('GO:0016765')
+		expect(go_term).not_to be_nil
+	end
+
+	it "Should return nil when a go term cannot be found by name" do
+	
+		go_term = @go.find_go('GO:0016765_noexiste')
+		expect(go_term).to be_nil
+	end
+
+	it "Should have 3 base terms without ancestors" do
+
+		expect(@go.base_terms.count).to eq(3)
+		expect(@go.base_terms.map(&:id)).to match_array(["GO:0003674", "GO:0005575", "GO:0008150"])
+
+		@go.base_terms.each do |baset|
+			expect(baset.ancestors.count).to be(0)
+		end
+		
+	end
+
+	it "Should convert a list of go names as strings to go terms " do
+		go_list=["GO:0003674", "GO:0005575", "GO:0008150"]
+
+		expect(@go.go_list_to_terms(go_list).count).to eq(go_list.count)
+		expect(@go.go_list_to_terms(go_list).map(&:id)).to match_array(["GO:0003674", "GO:0005575", "GO:0008150"])
+
+	end
+
+	it "Should not convert a list of go_terms" do
+		# use a list of go_terms
+		go_list=@go.base_terms
+		expect(@go.go_list_to_terms(go_list).map(&:id)).to match_array(["GO:0003674", "GO:0005575", "GO:0008150"])
+
+	end
+
+
+	it "Should convert a mix of go names as strings and go_terms to go_terms" do
+		
+		# use a list of go_terms
+		go_list = @go.base_terms
+		go_list << "GO:0009889"
+		expect(@go.go_list_to_terms(go_list).map(&:id)).to match_array(["GO:0003674", "GO:0005575", "GO:0008150", "GO:0009889"])
+	end
+
+end

data/spec/lib/go_list_reducer_spec.rb

@@ -0,0 +1,77 @@
+require 'spec_helper'
+
+describe ScbiGo::GoListReducer do
+	before(:all) do
+    	@glr=ScbiGo::GoListReducer.new
+  	end
+	
+	it "Should reduce a complete ordered branch to the lower GO" do
+		go_list = ["GO:2001141", "GO:0031326", "GO:0009889", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"]
+
+		g=@glr.reduce_branches(go_list);
+		expect(g.map(&:id)).to match_array(["GO:2001141"])
+	end
+
+	it "Should reduce a complete un-ordered branch to the lower GO" do
+		go_list = ["GO:0050789", "GO:0009889", "GO:0019222", "GO:0031326", "GO:0065007","GO:2001141", "GO:0008150"]
+
+		g=@glr.reduce_branches(go_list);
+		expect(g.count).to eq(1)
+		expect(g.map(&:id)).to match_array(["GO:2001141"])
+	end
+
+	#http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:2001141#term=ancchart
+	it "Should not reduce empty list" do
+		go_list=[]
+		g=@glr.reduce_branches(go_list);
+		expect(g.count).to eq(0)
+		expect(g.map(&:id)).to match_array([])
+	end
+
+	#http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0010556#term=ancchart
+	it "Should reduce a list of gos to only the leaves of their branches" do
+		
+		leaves=["GO:0010556", "GO:0019219"]
+		
+		input_go_list = ["GO:0010556", "GO:0060255", "GO:0019219"]
+
+		g=@glr.reduce_branches(input_go_list);
+
+		expect(g.map(&:id)).to match_array(leaves)
+	end
+
+
+	#http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:2001141#term=ancchart
+	it "For a list of gos, Should find best_matching branches" do
+		
+		original_go_paths = [["GO:2001141", "GO:0031326", "GO:0009889", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+		 ["GO:2001141", "GO:0031326", "GO:0031323", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"]]
+
+		input_go_list = ["GO:2001141", "GO:0031326", "GO:0019222", "GO:0065007", "GO:0008150"]
+
+		g=@glr.best_matching_branches(input_go_list);
+
+		expect(g.map{|e| e.map(&:id)}).to match_array(original_go_paths)
+	end
+
+	#http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:2001141#term=ancchart
+	it "Should get all matching branches for a list of input gos" do
+		
+		all_branches=[
+			["GO:0010556", "GO:0009889", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"],
+			["GO:0010556", "GO:0060255", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			["GO:0019219", "GO:0031323", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			["GO:0019219", "GO:0031323", "GO:0050794", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			["GO:0019219", "GO:0051171", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			["GO:0019219", "GO:0080090", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"]
+		]
+		
+
+		input_go_list = ["GO:0010556", "GO:0060255", "GO:0019219"]
+
+		g=@glr.all_matching_branches(input_go_list);
+
+		expect(g.map{|e| e.map(&:id)}).to match_array(all_branches)
+	end
+
+end

data/spec/lib/go_term_spec.rb

@@ -0,0 +1,90 @@
+require 'spec_helper'
+
+describe ScbiGo::GoTerm do
+	before(:all) do
+    	@go=ScbiGo::GeneOntology.new
+  	end
+
+	it "GO:0000011 Should have two is_a to their parents" do
+		term=@go.find_go('GO:0000011')
+
+		expect(term).not_to be_nil
+		expect(term.is_a.first).to be_a(ScbiGo::GoTerm)
+		expect(term.is_a.count).to eq(2)
+		expect(term.is_a.map(&:id)).to match_array(["GO:0007033", "GO:0048308"])
+	end
+
+	it "GO:0016765 Should have 67 children" do
+		term=@go.find_go('GO:0016765')
+
+		expect(term).not_to be_nil
+		expect(term.children.count).to eq(67)
+		expect(term.children.first).to be_a(ScbiGo::GoTerm)
+		expect(term.children.first.id).to eq('GO:0000010')
+		expect(term.children.last.id).to eq('GO:0098601')
+	end
+
+
+	it "GO:0016043 Should have 2 descendants with class GoTerm" do
+		term=@go.find_go('GO:0016043')
+		
+		expect(term.descendants.first).to be_a(ScbiGo::GoTerm)
+		expect(term.descendants.map(&:id)).to end_with ["GO:0075503", "GO:0072565"]
+	end
+
+	it "GO:0016043 Should have self and descendants" do
+		term=@go.find_go('GO:0016043')
+		expect(term.self_and_descendants.map(&:id)).to start_with [term.id]
+		expect(term.self_and_descendants.map(&:id)).to end_with ["GO:0075503", "GO:0072565"]
+	end
+
+
+	it "GO:0016043 Should have 2 ancestors with class GoTerm" do
+		term=@go.find_go('GO:0016043')
+		expect(term.ancestors.first).to be_a(ScbiGo::GoTerm)
+		expect(term.ancestors.map(&:id)).to end_with ["GO:0071840", "GO:0008150"]
+	end
+	
+	it "GO:0016043 Should have self and ancestors" do
+		term=@go.find_go('GO:0016043')
+		expect(term.self_and_ancestors.map(&:id)).to start_with [term.id]
+		expect(term.self_and_ancestors.map(&:id)).to end_with ["GO:0071840", "GO:0008150"]
+	end
+
+	#http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0050789#term=ancchart
+	it "GO:0050789 Should have only one branch to top" do
+		term=@go.find_go('GO:0050789')
+		expect(term.all_branches_to_top.map{|e| e.map(&:id)}).to match_array([['GO:0050789','GO:0065007','GO:0008150']])
+		expect(term.all_branches_to_top.count).to eq 1
+	end
+
+	#http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031323#term=ancchart
+	it "GO:0031323 Should have two branches to top" do
+		term=@go.find_go('GO:0031323')
+		expect(term.all_branches_to_top.map{|e| e.map(&:id)}).to match_array([["GO:0031323","GO:0019222","GO:0050789","GO:0065007","GO:0008150"],["GO:0031323","GO:0050794","GO:0050789","GO:0065007","GO:0008150"]])
+		expect(term.all_branches_to_top.count).to eq 2
+	end
+
+	it "GO:0003674 Should have a branch to top with only me" do
+		term=@go.find_go('GO:0003674')
+		expect(term.all_branches_to_top.map{|e| e.map(&:id)}).to match_array([["GO:0003674"]])
+	end
+
+	it "GO:2001141 Should have 10 branches to top" do
+		term=@go.find_go('GO:2001141')
+		expect(term.all_branches_to_top.count).to eq 10
+		res = [["GO:2001141", "GO:0010556", "GO:0009889", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0010556", "GO:0060255", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0031326", "GO:0009889", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0031326", "GO:0031323", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0031326", "GO:0031323", "GO:0050794", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0051252", "GO:0019219", "GO:0031323", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0051252", "GO:0019219", "GO:0031323", "GO:0050794", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0051252", "GO:0019219", "GO:0051171", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0051252", "GO:0019219", "GO:0080090", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"], 
+			 ["GO:2001141", "GO:0051252", "GO:0060255", "GO:0019222", "GO:0050789", "GO:0065007", "GO:0008150"]]
+
+		expect(term.all_branches_to_top.map{|e| e.map(&:id)}).to match_array(res)
+	end
+end
+

data/spec/lib/header_spec.rb

@@ -0,0 +1,12 @@
+require 'spec_helper'
+
+describe ScbiGo::Header do
+	before(:all) do
+    	@go=ScbiGo::GeneOntology.new
+  	end
+  	
+	it "Should load obo file version 1.2" do
+		expect(@go.header.format_version).to eq('1.2')
+	end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1 @@
+require 'scbi_go'

metadata

@@ -0,0 +1,148 @@
+--- !ruby/object:Gem::Specification
+name: scbi_go
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- dariogf
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-06-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: guard-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: obo
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: GeneOntology tools to summarize and graph go terms
+email:
+- dariogf@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".autotest"
+- ".gitignore"
+- Gemfile
+- Guardfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/data/go.obo.gz
+- lib/scbi_go.rb
+- lib/scbi_go/ancestors_graph.rb
+- lib/scbi_go/base_graph.rb
+- lib/scbi_go/descendants_graph.rb
+- lib/scbi_go/gene_ontology.rb
+- lib/scbi_go/go_list_reducer.rb
+- lib/scbi_go/go_term.rb
+- lib/scbi_go/header.rb
+- lib/scbi_go/version.rb
+- scbi_go.gemspec
+- spec/lib/ancestors_graph_spec.rb
+- spec/lib/base_graph_spec.rb
+- spec/lib/descendants_graph_spec.rb
+- spec/lib/gene_ontology_spec.rb
+- spec/lib/go_list_reducer_spec.rb
+- spec/lib/go_term_spec.rb
+- spec/lib/header_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.4
+signing_key: 
+specification_version: 4
+summary: GeneOntology tools.
+test_files:
+- spec/lib/ancestors_graph_spec.rb
+- spec/lib/base_graph_spec.rb
+- spec/lib/descendants_graph_spec.rb
+- spec/lib/gene_ontology_spec.rb
+- spec/lib/go_list_reducer_spec.rb
+- spec/lib/go_term_spec.rb
+- spec/lib/header_spec.rb
+- spec/spec_helper.rb