bio-jaspar 0.1.0

checksums.yaml

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+SHA1:
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+  data.tar.gz: 98b718e4a029fec3389078213fd7ab5613f89c38
+SHA512:
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data/.document

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

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "bio", ">= 1.4.2"
+gem "mysql2", "~> 0.3.19"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+	gem "shoulda", ">= 0"
+  gem "rake", "~> 0.9.3"
+  gem "rdoc", "~> 3.12"
+  gem 'test-unit'
+  gem "jeweler", "~> 2.0.1", :git => "https://github.com/technicalpickles/jeweler.git"
+  gem "bundler", ">= 1.0.21"
+end

data/LICENSE.txt

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+Copyright (c) 2015 Wasserman Lab
+
+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

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+# bio-jaspar
+
+## Tools for JASPAR motif analysis
+
+This gem provides methods for: 
+
+1. Reading and writing sequence motifs in JASPAR format
+2. Accessing a JASPAR5 formatted database
+3. Comparing, searching, and analyzing motifs in sequences
+
+<sup>*</sup> **Note:** The JASPAR motif analysis tools consist of several modules that are directly imported from the Bio.motifs package in BioPython. Namely, those modules/submodules are: Bio.motifs, Bio.motifs.matrix, Bio.motifs.thresholds, Bio.motifs.jaspar. The functionality of this gem will be identical to the aforementioned modules/submodules.
+
+
+## Installation
+
+```sh
+gem install bio-jaspar
+```
+
+## Usage
+
+### Loading the gem
+
+```ruby
+require 'bio-jaspar'
+```
+
+### Loading a motif/motifs from a JASPAR database
+
+A connection to the JASPAR database is made by creating a JASPAR5 instance.
+
+```ruby
+# Substitute the database credentials!
+db = Bio::Jaspar::JASPAR5.new(
+	:host => <db_host.org>,
+	:name => <db_name>,
+	:user => <db_user>,
+	:password => <db_password>
+)
+```
+
+Now, a motif can be retrieved by the matrix_id
+
+```ruby
+m = db.fetch_motif_by_id("MA0049")
+puts m.to_s
+```
+
+Or multiple motifs can be retrieved by various criteria
+
+```ruby
+motifs = db.fetch_motifs(
+	:collection => "CORE",
+	:tax_group => ["fungi", "vertebrate"],
+	:tf_class => "Helix-Turn-Helix",
+	:min_ic => 2
+)
+motifs.each { |m| # do something with a motif }
+```
+
+### Motif analysis
+
+Many methods are available for motif analysis. Here are some examples:
+
+```ruby
+m = db.fetch_motif_by_id("MA0049")
+
+# Consensus sequence
+m.consensus 					# BioRuby Sequence object
+puts m.consensus
+
+# Anticonsensus sequence
+m.anticonsensus				# BioRuby Sequence object
+puts m.anticonsensus
+
+# Reverse complement motif
+m.reverse_complement	# Bio::Motif::Motifs object
+
+# Pseudocounts
+m.pseudocounts
+
+# Background
+m.background
+
+# Position weight matrix
+m.pwm
+
+# Position specific scoring matrix
+m.pssm
+```
+
+Matrix methods are also available. Here are some examples:
+
+```ruby
+m = db.fetch_motif_by_id("MA0049")
+
+# Maximum possible score for the given motif
+m.pssm.max
+
+# Minimum possible score for the given motif
+m.pssm.min
+
+# Expected value of the motif score
+m.pssm.mean
+
+# Standard deviation of the given motif score
+m.pssm.std
+
+# Find hits with the PWM score above given threshold
+m.pssm.search(Bio::Sequence.auto("ACCTGCCTAAAAAA"), threshold = 0.5)
+```
+
+### Read/write Jaspar file
+
+Already downloaded pfm, jaspar, sites files can be loaded/written using the Jaspar module
+
+```ruby
+# Read a pfm file
+f = File.open("test.pfm", "r")
+Bio::Jaspar.read(f, "pfm")
+f.close
+
+# Write motifs into a jaspar file
+motifs = db.fetch_motifs(
+	:collection => "CORE",
+	:tax_group => ["fungi", "vertebrate"],
+	:tf_class => "Helix-Turn-Helix",
+	:min_ic => 2
+)
+File.open("test.jaspar", "w") do |f|
+	Bio::Jaspar.write(f, "jaspar")
+end
+```
+
+Please refer to the rdoc for full information on all available methods & classes.
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wassermanlab/jaspar-bioruby
+
+## Copyright
+
+See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-jaspar
+
+== Tools for JASPAR motif analysis
+
+This gem provides methods for: 
+
+1. Reading and writing sequence motifs in JASPAR format
+2. Accessing a JASPAR5 formatted database
+3. Comparing, searching, and analyzing motifs in sequences
+
+\* *Note:* The JASPAR motif analysis tools consist of several modules that are directly imported from the Bio.motifs package in BioPython. Namely, those modules/submodules are: Bio.motifs, Bio.motifs.matrix, Bio.motifs.thresholds, Bio.motifs.jaspar. The functionality of this gem will be identical to the aforementioned modules/submodules.
+
+== Installation
+
+        gem install bio-jaspar
+
+== Usage
+
+=== Loading the gem
+
+		require 'bio-jaspar'
+
+=== Loading a motif/motifs from a JASPAR database
+
+A connection to the JASPAR database is made by creating a JASPAR5 instance.
+
+		# Substitute the database credentials!
+		db = Bio::Jaspar::JASPAR5.new(
+			:host => <db_host.org>,
+			:name => <db_name>,
+			:user => <db_user>,
+			:password => <db_password>
+		)
+
+Now, a motif can be retrieved by the matrix_id
+
+		m = db.fetch_motif_by_id("MA0049")
+		puts m.to_s
+
+Or multiple motifs can be retrieved by various criteria
+
+		motifs = db.fetch_motifs(
+			:collection => "CORE",
+			:tax_group => ["fungi", "vertebrate"],
+			:tf_class => "Helix-Turn-Helix",
+			:min_ic => 2
+		)
+
+=== Motif analysis
+
+Many methods are available for motif analysis. Here are some examples:
+		
+		m = db.fetch_motif_by_id("MA0049")
+
+		# Consensus sequence
+		m.consensus 					# BioRuby Sequence object
+		puts m.consensus
+
+		# Anticonsensus sequence
+		m.anticonsensus				# BioRuby Sequence object
+		puts m.anticonsensus
+
+		# Reverse complement motif
+		m.reverse_complement	# Bio::Motif::Motifs object
+
+		# Pseudocounts
+		m.pseudocounts
+
+		# Background
+		m.background
+
+		# Position weight matrix
+		m.pwm
+
+		# Position specific scoring matrix
+		m.pssm
+
+Matrix methods are also available. Here are some examples:
+
+		m = db.fetch_motif_by_id("MA0049")
+
+		# Maximum possible score for the given motif
+		m.pssm.max
+
+		# Minimum possible score for the given motif
+		m.pssm.min
+
+		# Expected value of the motif score
+		m.pssm.mean
+
+		# Standard deviation of the given motif score
+		m.pssm.std
+
+		# Find hits with the PWM score above given threshold
+		m.pssm.search(Bio::Sequence.auto("ACCTGCCTAAAAAA"), threshold = 0.5)
+
+=== Read/write Jaspar file
+
+Already downloaded pfm, jaspar, sites files can be loaded/written using the Jaspar module
+
+		# Read a pfm file
+		f = File.open("test.pfm", "r")
+		Bio::Jaspar.read(f, "pfm")
+		f.close
+
+		# Write motifs into a jaspar file
+		motifs = db.fetch_motifs(
+			:collection => "CORE",
+			:tax_group => ["fungi", "vertebrate"],
+			:tf_class => "Helix-Turn-Helix",
+			:min_ic => 2
+		)
+		File.open("test.jaspar", "w") do |f|
+			Bio::Jaspar.write(f, "jaspar")
+		end
+
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/wassermanlab/jaspar-bioruby
+
+== Copyright
+
+See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+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://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-jaspar"
+  gem.homepage = "http://github.com/wassermanlab/jaspar-bioruby"
+  gem.license = "MIT"
+  gem.summary = %Q{Tools for JASPAR motifs in BioRuby}
+  gem.description = %Q{Basic tools for parsing, searching, and comparing JASPAR motifs; Based on Bio.motifs module in Biopython}
+  gem.authors = ["Jessica Lee", "Wasserman Lab"]
+  # dependencies defined in Gemfile
+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
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-jaspar #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+  rdoc.main = "README.rdoc"
+end

data/lib/bio-jaspar.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-jaspar/motifs.rb'
+require 'bio-jaspar/matrix.rb'
+require 'bio-jaspar/thresholds.rb'
+require 'bio-jaspar/jaspar.rb'
+require 'bio-jaspar/db.rb'

data/lib/bio-jaspar/jaspar.rb

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+#--
+# = bio-jaspar/jaspar.rb 
+# 
+# Copyright:: (C) 2015-2015 Wasserman Lab
+# License:: Ruby License
+# 
+# JASPAR 2014 module
+# 
+# A direct import of Bio.motifs.jaspar module in Biopython
+#++
+
+require 'bio'
+
+module Bio # :nodoc:
+	# == JASPAR 2014 module
+	# 
+	# Provides read access to a JASPAR5 formatted database.
+	# 
+	# This module is a direct import of Bio.motifs.jaspar module in Biopython.
+	# The following document contains excerpts from Bio.motifs.jaspar module 
+	# in Biopython.
+	module Jaspar
+
+		# Unambiguous DNA bases
+		DNA = Bio::Motifs::Alphabet.new.IUPAC_unambiguous_dna
+
+		# JASPAR OUTPUT specific DNA bases
+		JASPAR_ORDERED_DNA_LETTERS = ["A","C","G","T"] # Jaspar requires specific order for printouts
+
+		# A subclass of Bio::Motifs::Motif used to represent a JASPAR profile.
+		# 
+    # Additional metadata information are stored if available. The metadata
+    # availability depends on the source of the JASPAR motif (a 'pfm' format
+    # file, a 'jaspar' format file or a JASPAR database).
+    # 
+    # <i>A direct import of Bio.motifs.jaspar module in Biopython</i>
+		class Motif < Bio::Motifs::Motif
+			attr_accessor :matrix_id, :collection, :tf_class, :tf_family, :species,
+										:tax_group, :acc, :data_type, :medline, :pazar_id, :comment
+
+			# Construct a JASPAR Motif instance
+			# 
+			def initialize(matrix_id, name, opts = {})
+				opts = {
+					:alphabet => DNA, 
+					:instances => nil, 
+					:counts => nil, 
+					:collection => nil, 
+					:tf_class => nil, 
+					:tf_family => nil, 
+					:species => nil, 
+					:tax_group => nil, 
+					:acc => nil, 
+					:data_type => nil, 
+					:medline => nil, 
+					:pazar_id => nil, 
+					:comment => nil
+				}.merge(opts)
+
+				super(opts[:alphabet], opts[:instances], opts[:counts])
+
+				@name = name
+				@matrix_id = matrix_id
+				@collection = opts[:collection]
+				@tf_class = opts[:tf_class]
+				@tf_family = opts[:tf_family]
+				@species = opts[:species]
+				@tax_group = opts[:tax_group]
+				@acc = opts[:acc]
+				@data_type = opts[:data_type]
+				@medline = opts[:medline]
+				@pazar_id = opts[:pazar_id]
+				@comment = opts[:comment]
+			end
+
+			# Return the JASPAR base matrix ID
+			def base_id
+				base_id, _ = Jaspar.split_jaspar_id(@matrix_id)
+				return base_id
+			end
+
+			# Return the JASPAR matrix version
+			def version
+				_, version = Jaspar.split_jaspar_id(@matrix_id)
+				return version
+			end
+
+			# Return a string represention of the JASPAR profile.
+			#
+      # We choose to provide only the filled metadata information.
+			def to_s
+				tf_name_str = "TF name\t#{@name}\n"
+				matrix_id_str = "Matrix ID\t#{@matrix_id}\n"
+				the_string = tf_name_str + matrix_id_str
+
+				if @collection
+					collection_str = "Collection\t#{@collection}\n"
+					the_string += collection_str
+				end
+        if @tf_class
+          tf_class_str = "TF class\t#{@tf_class}\n"
+          the_string += tf_class_str
+        end
+        if @tf_family
+          tf_family_str = "TF family\t#{@tf_family}\n"
+          the_string += tf_family_str
+        end
+        if @species
+          species_str = "Species\t#{@species.join(",")}\n"
+          the_string += species_str
+        end
+        if @tax_group
+          tax_group_str = "Taxonomic group\t#{@tax_group}\n"
+          the_string += tax_group_str
+        end
+        if @acc
+          acc_str = "Accession\t#{@acc}\n"
+          the_string += acc_str
+        end
+        if @data_type
+          data_type_str = "Data type used\t#{@data_type}\n"
+          the_string += data_type_str
+        end
+        if @medline
+          medline_str = "Medline\t#{@medline}\n"
+          the_string += medline_str
+        end
+        if @pazar_id
+          pazar_id_str = "PAZAR ID\t#{@pazar_id}\n"
+          the_string += pazar_id_str
+        end
+        if @comment
+          comment_str = "Comments\t#{@comment}\n"
+          the_string += comment_str
+        end
+        matrix_str = "Matrix:\n#{counts}\n\n"
+        the_string += matrix_str
+        return the_string
+			end
+
+			# Return the hash key corresponding to the JASPAR profile
+			#
+      # Note: We assume the unicity of matrix IDs
+			def hash
+				return @matrix_id.hash
+			end
+
+			# Compare two JASPAR motifs for equality. Two motifs are equal if their
+			# matrix_ids match
+			def ==(other)
+				return @matrix_id == other.matrix_id
+			end
+
+		end
+
+		# Represent a list of JASPAR motifs.
+		#
+		# <i>A direct import of Bio.motifs.jaspar module in Biopython</i>
+    # 
+    # ==== Attributes
+    #
+    # * +version+ - The JASPAR version used
+		class Record < Array
+			# Construct a record instance
+			def initialize
+				super()
+				@version = nil
+			end
+
+			# Return a string of all JASPAR motifs in the list
+			def to_s
+				return self.map { |the_motif| the_motif.to_s }.join("\n")
+			end
+
+			# Return the list of matrices as a hash (ruby equivalent of dict)
+			# of matrices
+			def to_h
+				dic = {}
+				self.each { |motif|
+					dic[motif.matrix_id] = motif
+				}
+				return dic
+			end
+		end
+
+		# Read motif(s) from a file in one of several different JASPAR formats.
+		# 
+    # Return the record of PFM(s).
+    # Call the appropriate routine based on the format passed
+		def Jaspar.read(handle, format)
+			format = format.downcase
+			if format == "pfm"
+				record = _read_pfm(handle)
+				return record
+			elsif format == "sites"
+				record = _read_sites(handle)
+				return record
+			elsif format == "jaspar"
+				record = _read_jaspar(handle)
+				return record
+			else
+				raise ArgumentError, "Unknown JASPAR format #{format}"
+			end
+					
+		end
+
+		# Return the representation of motifs in "pfm" or "jaspar" format.
+		def Jaspar.write(motifs, format)
+			letters = JASPAR_ORDERED_DNA_LETTERS
+			lines = []
+			if format == "pfm"
+				motif = motifs[0]
+				counts = motif.counts
+				letters.each do |letter|
+					terms = counts[letter].map { |value| "%6.2f" % value }
+					line = "#{terms.join(" ")}\n"
+					lines << line
+				end
+			elsif format == "jaspar"
+				motifs.each do |m|
+					counts = m.counts
+					line = ">#{m.matrix_id} #{m.name}\n"
+					lines << line
+
+					letters.each do |letter|
+						terms = counts[letter].map { |value| "%6.2f" % value }
+						line = "#{letter} [#{terms.join(" ")}]\n"
+						lines << line
+					end
+				end
+			else
+				raise ArgumentError, "Unknown JASPAR format #{format}"
+			end
+				
+			text = lines.join("")
+			return text	
+		end
+
+		# Return pseudocounts of a given JASPAR motif
+		def Jaspar.calculate_pseudocounts(motif)
+			alphabet = motif.alphabet
+			background = motif.background
+
+			total = 0
+			(0...motif.length).each do |i|
+				total += alphabet.letters.map { |letter| motif.counts[letter][i].to_f }.inject(:+)
+			end
+
+			avg_nb_instances = total / motif.length
+			sq_nb_instances = Math.sqrt(avg_nb_instances)
+
+			if background
+				background = Hash[background]
+			else
+				background = Hash[alphabet.letters.sort.map { |l| [l, 1.0] }]
+			end
+
+			total = background.values.inject(:+)
+			pseudocounts = {}
+
+			alphabet.letters.each do |letter|
+				background[letter] /= total
+				pseudocounts[letter] = sq_nb_instances * background[letter]
+			end
+
+			return pseudocounts
+		end
+
+		# Utility function to split a JASPAR matrix ID into its component.
+		#
+    # Components are base ID and version number, e.g. 'MA0047.2' is returned as
+    # ('MA0047', 2).
+		def Jaspar.split_jaspar_id(id)
+			id_split = id.split(".")
+
+			base_id = nil
+			version = nil
+
+			if id_split.length == 2
+				base_id = id_split[0]
+				version = id_split[1]
+			else
+				base_id = id
+			end
+
+			return base_id, version
+		end
+
+		# Private methods
+		private
+
+		# Read the motif from a JASPAR .pfm file (PRIVATE).
+		def Jaspar._read_pfm(handle)
+			alphabet = DNA
+			counts = {}
+
+			letters = JASPAR_ORDERED_DNA_LETTERS
+			letters.zip(handle).each do |letter, line|
+				words = line.split
+				if words[0] == letter
+					words = words[1..-1]
+				end
+				counts[letter] = words.map(&:to_f)
+			end
+
+			motif = Motif.new(nil, nil, :alphabet => alphabet, :counts => counts)
+			motif.mask = "*" * motif.length
+			record = Record.new
+			record << motif
+
+			return record
+		end
+
+		# Read the motif from JASPAR .sites file (PRIVATE).
+		def Jaspar._read_sites(handle)
+			alphabet = DNA
+			instances = []
+
+			handle_enum = handle.to_enum
+
+			handle.each do |line|
+				unless line.start_with?(">")
+					break
+				end
+
+				line = handle_enum.next
+				instance = ""
+				line.strip.each_char do |c|
+					if c == c.upcase
+						instance += c
+					end
+				end
+				instance = Bio::Sequence.auto(instance)
+				instances << instance
+			end
+
+			instances = Bio::Motifs::Instances.new(instances, alphabet)
+			motif = Motif.new(nil, nil, :alphabet => alphabet, :instances => instances)
+			motif.mask = "*" * motif.length
+			record = Record.new
+			record << motif
+
+			return record
+		end
+
+		# Read motifs from a JASPAR formatted file (PRIVATE).
+		# 
+    # Format is one or more records of the form, e.g.::
+    # 
+    #   - JASPAR 2010 matrix_only format::
+    #
+    #             >MA0001.1 AGL3
+    #             A  [ 0  3 79 40 66 48 65 11 65  0 ]
+    #             C  [94 75  4  3  1  2  5  2  3  3 ]
+    #             G  [ 1  0  3  4  1  0  5  3 28 88 ]
+    #             T  [ 2 19 11 50 29 47 22 81  1  6 ]
+    #
+    #   - JASPAR 2010-2014 PFMs format::
+    #
+    #             >MA0001.1 AGL3
+    #             0	3	79	40	66	48	65	11	65	0
+    #             94	75	4	3	1	2	5	2	3	3
+    #             1	0	3	4	1	0	5	3	28	88
+    #             2	19	11	50	29	47	22	81	1	6
+    #             
+		def Jaspar._read_jaspar(handle)
+			alphabet = DNA
+			counts = {}
+
+			record = Record.new
+
+			head_pat = /^>\s*(\S+)(\s+(\S+))?/
+			row_pat_long = /\s*([ACGT])\s*\[\s*(.*)\s*\]/
+			row_pat_short = /\s*(.+)\s*/
+
+			identifier = nil
+			name = nil
+			row_count = 0
+			nucleotides = ["A","C","G","T"]
+			handle.each do |line|
+				line = line.strip
+				
+				head_match = line.match(head_pat)
+				row_match_long = line.match(row_pat_long)
+				row_match_short = line.match(row_pat_short)
+
+				if head_match
+					identifier = head_match[1]
+					if head_match[3]
+						name = head_match[3]
+					else
+						name = identifier
+					end
+				elsif row_match_long
+					letter, counts_str = row_match_long[1..2]
+					words = counts_str.split
+					counts[letter] = words.map(&:to_f)
+					row_count += 1
+					if row_count == 4
+						record << Motif.new(identifier, 
+						                    name, 
+						                    :alphabet => alphabet, 
+						                    :counts => counts)
+						identifier = nil
+						name = nil
+						counts = {}
+						row_count = 0
+					end
+				elsif row_match_short
+					words = row_match_short[1].split
+					counts[nucleotides[row_count]] = words.map(&:to_f)
+					row_count += 1
+					if row_count == 4
+						record << Motif.new(identifier, 
+						                    name, 
+						                    :alphabet => alphabet, 
+						                    :counts => counts)
+						identifier = nil
+						name = nil
+						counts = {}
+						row_count = 0
+					end
+				end		
+			end
+
+			return record
+		end
+
+		private_class_method :_read_pfm, :_read_sites, :_read_jaspar
+
+	end
+end

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-jaspar'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-jaspar.rb

@@ -0,0 +1,265 @@
+require 'helper'
+require 'bio-jaspar'
+require 'bio'
+
+class TestBioJaspar < Test::Unit::TestCase
+  context 'JASPAR module' do
+  	should "correctly read jaspar formatted file" do
+  		f = File.open('test/data/jaspar-test.jaspar', "r") 
+			motifs = Bio::Motifs.parse(f, "jaspar")
+			f.close
+
+			# Test first motif in the set
+			corr_motifs_beg_counts = {
+				"A" => [3.0, 21.0, 25.0, 0.0, 0.0, 24.0, 1.0, 0.0], 
+				"C" => [13.0, 1.0, 0.0, 0.0, 5.0, 0.0, 0.0, 0.0], 
+				"T" => [5.0, 3.0, 0.0, 25.0, 20.0, 0.0, 24.0, 23.0], 
+				"G" => [4.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0]
+			}
+			assert_equal corr_motifs_beg_counts, motifs[0].counts
+			assert_equal 8, motifs[0].length
+			assert_equal "HAT5", motifs[0].name
+			assert_equal "MA0008.1", motifs[0].matrix_id
+
+			# Test the last motif in the set
+			corr_motifs_end_counts = {
+				"A" => [4.0, 5.0, 5.0, 3.0, 0.0, 0.0, 25.0, 26.0, 0.0, 0.0, 26.0, 0.0, 0.0, 17.0, 0.0, 5.0, 2.0, 0.0, 0.0], 
+				"C" => [2.0, 3.0, 4.0, 8.0, 1.0, 6.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 25.0, 1.0, 6.0, 3.0, 5.0], 
+				"T" => [2.0, 3.0, 5.0, 5.0, 0.0, 20.0, 0.0, 0.0, 26.0, 0.0, 0.0, 26.0, 23.0, 0.0, 0.0, 7.0, 4.0, 3.0, 0.0], 
+				"G" => [1.0, 3.0, 2.0, 2.0, 25.0, 0.0, 1.0, 0.0, 0.0, 26.0, 0.0, 0.0, 3.0, 9.0, 1.0, 4.0, 0.0, 4.0, 3.0]
+			}
+			assert_equal corr_motifs_end_counts, motifs[-1].counts
+			assert_equal 19, motifs[-1].length
+			assert_equal "ATHB9", motifs[-1].name
+			assert_equal "MA0573.1", motifs[-1].matrix_id
+  	end
+
+  	should "correctly read pfm formatted file" do
+  		f = File.open('test/data/jaspar-test.pfm', "r") 
+			motif = Bio::Motifs.parse(f, "pfm")
+			f.close
+
+			corr_counts = {
+				"A" => [3.0, 21.0, 25.0, 0.0, 0.0, 24.0, 1.0, 0.0], 
+				"C" => [13.0, 1.0, 0.0, 0.0, 5.0, 0.0, 0.0, 0.0], 
+				"T" => [5.0, 3.0, 0.0, 25.0, 20.0, 0.0, 24.0, 23.0], 
+				"G" => [4.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0]
+			}
+			assert_equal 1, motif.length # should only read one motif
+			assert_equal 8, motif[0].length
+			assert_equal corr_counts, motif[0].counts
+  	end
+
+  	should "correctly read sites formatted file" do
+  		f = File.open('test/data/jaspar-test.sites', "r") 
+			motif = Bio::Motifs.parse(f, "sites")
+			f.close
+
+			corr_counts = {
+				"A" => [15, 4, 41, 36, 7, 19, 3], 
+				"C" => [11, 35, 1, 2, 29, 14, 22], 
+				"T" => [7, 2, 0, 1, 1, 3, 3], 
+				"G" => [10, 2, 1, 4, 6, 7, 15]
+			}
+			assert_equal 7, motif[0].length
+			assert_equal corr_counts, motif[0].counts
+
+			# Check the first and last sequence motifs
+			assert_equal "ccaaccc", motif[0].instances[0].to_s
+			assert_equal "gtatctc", motif[0].instances[-1].to_s
+  	end
+
+  end
+
+  # Once the reads pass the test, load the test files and setup the test
+	setup do
+		f = File.open('test/data/jaspar-test.jaspar', "r") 
+		@motifs = Bio::Motifs.parse(f, "jaspar")
+		@motif = @motifs.first
+		f.close
+	end
+
+	context 'JASPAR module' do
+  	should "correctly convert Motifs into jaspar formatted string" do
+  		corr_jaspar = ">MA0008.1 HAT5\nA [  3.00  21.00  25.00   0.00   0.00  24.00   1.00   0.00]\nC [ 13.00   1.00   0.00   0.00   5.00   0.00   0.00   0.00]\nG [  4.00   0.00   0.00   0.00   0.00   1.00   0.00   2.00]\nT [  5.00   3.00   0.00  25.00  20.00   0.00  24.00  23.00]\n>MA0027.1 En1\nA [  4.00   5.00   3.00   0.00   4.00   3.00   3.00   2.00   1.00   1.00   1.00]\nC [  1.00   2.00   0.00   0.00   0.00   0.00   0.00   1.00   3.00   4.00   6.00]\nG [  2.00   2.00   7.00   2.00   3.00   7.00   0.00   4.00   3.00   1.00   1.00]\nT [  3.00   1.00   0.00   8.00   3.00   0.00   7.00   3.00   3.00   4.00   2.00]\n>MA0046.1 HNF1A\nA [  5.00   1.00   1.00   1.00  20.00  16.00   1.00   8.00  14.00   2.00   0.00  13.00   8.00   5.00]\nC [  0.00   0.00   0.00   0.00   0.00   2.00   0.00   2.00   0.00   0.00   4.00   1.00   8.00  13.00]\nG [ 14.00  20.00   0.00   0.00   0.00   1.00   0.00   4.00   1.00   0.00   0.00   3.00   3.00   0.00]\nT [  2.00   0.00  20.00  20.00   1.00   2.00  20.00   7.00   6.00  19.00  17.00   4.00   2.00   3.00]\n"
+  		jaspar = Bio::Jaspar.write(@motifs[0, 3], "jaspar")
+  		assert_equal corr_jaspar, jaspar
+  	end
+
+  	should "correctly convert Motifs into pfm formatted string" do
+  		corr_pfm = "  3.00  21.00  25.00   0.00   0.00  24.00   1.00   0.00\n 13.00   1.00   0.00   0.00   5.00   0.00   0.00   0.00\n  4.00   0.00   0.00   0.00   0.00   1.00   0.00   2.00\n  5.00   3.00   0.00  25.00  20.00   0.00  24.00  23.00\n"
+  		pfm = Bio::Jaspar.write(@motifs, "pfm")
+  		assert_equal corr_pfm, pfm
+  	end
+
+  	should "correctly calculate pseudocounts" do
+  		corr_pc = {"A" => 1.25, "C" => 1.25, "T" => 1.25, "G" => 1.25}
+  		pc = Bio::Jaspar.calculate_pseudocounts(@motifs[0])
+  		assert_equal corr_pc, pc
+  	end
+  end
+
+  context 'JASPAR Motif class' do
+		should "return a correct length" do
+			assert_equal 8, @motif.length
+		end
+
+	  should "return a correct consensus sequence" do
+	  	assert_equal Bio::Sequence.auto("CAATTATT").to_s, @motif.consensus.to_s
+	  end
+
+	  should "return a correct anticonsensus sequence" do
+	  	assert_equal Bio::Sequence.auto("AGGGGTGA").to_s, @motif.anticonsensus.to_s
+	  end
+
+	  should "return a correct degenerate consensus" do
+	  	assert_equal Bio::Sequence.auto("CAATTATT").to_s, @motif.degenerate_consensus.to_s
+	  end
+
+	  should "return a correct reverse complement" do
+	  	corr_rc_counts = {
+	  		"A" => [23.0, 24.0, 0.0, 20.0, 25.0, 0.0, 3.0, 5.0], 
+	  		"C" => [2.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 4.0], 
+	  		"T" => [0.0, 1.0, 24.0, 0.0, 0.0, 25.0, 21.0, 3.0], 
+	  		"G" => [0.0, 0.0, 0.0, 5.0, 0.0, 0.0, 1.0, 13.0]
+	  	}
+	  	rc = @motif.reverse_complement
+	  	assert_equal 0.13, rc.counts.gc_content
+	  	assert_equal 8, rc.length
+	  	assert_equal corr_rc_counts, rc.counts
+		end
+
+		should "return a correct mask" do
+			assert_equal [1,1,1,1,1,1,1,1], @motif.mask
+		end
+
+		should "return correct pseudocounts" do
+			corr_pc = {"A" => 0.0, "C" => 0.0, "T" => 0.0, "G" => 0.0}
+			assert_equal corr_pc, @motif.pseudocounts
+		end
+
+		should "return a correct background" do
+			corr_bg = {"A" => 0.25, "C" => 0.25, "T" => 0.25, "G" => 0.25}
+			assert_equal corr_bg, @motif.background
+		end
+
+		should "return a correct pwm" do
+			corr_pwm = {
+				"A" => [0.12, 0.84, 1.0, 0.0, 0.0, 0.96, 0.04, 0.0],
+				"C" => [0.52, 0.04, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0],
+				"T" => [0.2, 0.12, 0.0, 1.0, 0.8, 0.0, 0.96, 0.92],
+				"G" => [0.16, 0.0, 0.0, 0.0, 0.0, 0.04, 0.0, 0.08]
+			}
+			assert_equal corr_pwm, @motif.pwm
+		end
+
+		should "return a correct pssm" do
+			corr_pssm = {
+				"A" => [-1.0588936890535685, 1.7484612330040357, 2.0, -Float::INFINITY, -Float::INFINITY, 1.9411063109464317, -2.643856189774725, -Float::INFINITY], 
+				"C" => [1.0565835283663676, -2.643856189774725, -Float::INFINITY, -Float::INFINITY, -0.3219280948873623, -Float::INFINITY, -Float::INFINITY, -Float::INFINITY], 
+				"T" => [-0.3219280948873623, -1.0588936890535685, -Float::INFINITY, 2.0, 1.6780719051126378, -Float::INFINITY, 1.9411063109464317, 1.8797057662822885], 
+				"G" => [-0.6438561897747247, -Float::INFINITY, -Float::INFINITY, -Float::INFINITY, -Float::INFINITY, -2.643856189774725, -Float::INFINITY, -1.6438561897747248]
+			}
+			assert_equal corr_pssm, @motif.pssm
+		end
+
+		should "correctly format motif in jaspar format" do
+			corr_jaspar_str = ">MA0008.1 HAT5\nA [  3.00  21.00  25.00   0.00   0.00  24.00   1.00   0.00]\nC [ 13.00   1.00   0.00   0.00   5.00   0.00   0.00   0.00]\nG [  4.00   0.00   0.00   0.00   0.00   1.00   0.00   2.00]\nT [  5.00   3.00   0.00  25.00  20.00   0.00  24.00  23.00]\n"
+			assert_equal corr_jaspar_str, @motif.format("jaspar")
+		end
+
+		should "correctly format motif in pfm format" do
+			corr_pfm_str = "  3.00  21.00  25.00   0.00   0.00  24.00   1.00   0.00\n 13.00   1.00   0.00   0.00   5.00   0.00   0.00   0.00\n  4.00   0.00   0.00   0.00   0.00   1.00   0.00   2.00\n  5.00   3.00   0.00  25.00  20.00   0.00  24.00  23.00\n"
+			assert_equal corr_pfm_str, @motif.format("pfm")
+		end
+
+  end
+
+  context "matrix" do
+  	setup do
+			@motif2 = @motifs[1]
+			@non_inf_dist = @motifs[15].pssm.distribution
+		end
+
+  	should "correctly return maximum possible score" do
+  		assert_equal 14.245035054658192, @motif.pssm.max
+  	end
+
+  	should "correctly return the minimum possible score" do
+  		assert_equal -Float::INFINITY, @motif.pssm.min
+  	end
+
+  	should "correctly refuse fraction gc content calculation on pssm" do
+  		assert_raise do
+  			@motif.pssm.gc_content
+  		end
+  	end
+
+  	should "correctly calculate the mean" do
+  		assert_equal 11.882147864914165, @motif.pssm.mean
+  	end
+
+  	should "correctly calculate the std" do
+  		assert_equal 2.315187013634166, @motif.pssm.std
+  	end
+
+  	should "correctly calculates the PWM score for the given sequence" do
+  		corr_res = [-Float::INFINITY, -Float::INFINITY, -Float::INFINITY, 4.7579989]
+  		res = @motif.pssm.calculate(Bio::Sequence.auto("AGTTAATTAAG")).map{ |a| 
+  			if a.infinite?
+  				a
+  			else
+  				(a * (10 ** 7)).floor / (10.0 ** 7)
+  			end 
+  		}
+  		assert_equal corr_res, res
+  	end
+
+  	should "correctly search and return the position of the hits with PWM higher than threshold" do
+  		corr_hits = [[3, 4.7579989]]
+  		hits = @motif.pssm.search(Bio::Sequence.auto("AGTTAATTAAG")).map{ |a, b| 
+  			[a, (b * 10 ** 7).floor / (10.0 ** 7)]
+  		}
+  		assert_equal corr_hits, hits
+  	end
+
+  	should "correctly compare sequences using Pearson's correlation" do
+  		corr_pearson = [0.024879199790793116, -10]
+  		assert_equal corr_pearson, @motif.pssm.dist_pearson(@motif2.pssm)
+  	end
+
+  	should "correctly generate a distribution for non-infinite pssms" do
+  		assert_equal -54.665224748002345, @non_inf_dist.min_score
+  		assert_equal 15000, @non_inf_dist.n_points
+  		assert_equal 77.64489601267111, @non_inf_dist.interval
+  		assert_equal 0.005176671512278893, @non_inf_dist.step
+
+  		corr_md_beg_100 = [3.2600762748340303e-26, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 3.4153180022070797e-26, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 3.61062211083769e-26, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 3.782556497068055e-26, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 4.075095343542538e-26, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 4.269147502758849e-26, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 4.410691430657807e-26, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 4.5132776385471104e-26, 0.0, 0.0, 0.0, 0.0, 4.620724355927226e-26, 0.0, 0.0, 0.0, 0.0, 0.0]
+  		corr_md_end_100 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.006362547198123186, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.007703187540387484]
+  		assert_equal corr_md_beg_100, @non_inf_dist.mo_density[0, 100]
+  		assert_equal corr_md_end_100, @non_inf_dist.mo_density[@non_inf_dist.mo_density.length-100, 100]
+
+  		corr_bd_beg_100 = [9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0]
+  		corr_bd_end_100 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 9.313225746154785e-10]
+  		assert_equal corr_bd_beg_100, @non_inf_dist.bg_density[0, 100]
+  		assert_equal corr_bd_end_100, @non_inf_dist.bg_density[@non_inf_dist.bg_density.length-100, 100]
+  	end
+
+  	should "correctly calculate the threshold for false positive rate" do
+  		assert_equal -11.00517721344216, @non_inf_dist.threshold_fpr(0.1)
+  	end
+
+  	should "correctly calculate the threshold for false negative rate" do
+  		assert_equal 8.655821190193073, @non_inf_dist.threshold_fnr(0.1)
+  	end
+
+  	should "correctly calculate the balanced threshold" do
+  		assert_equal 0.3058500408872149, @non_inf_dist.threshold_balanced()
+  	end
+  	
+  	should "correctly calculate the patser threshold" do
+  		assert_equal 11.435693792286841, @non_inf_dist.threshold_patser()
+  	end
+
+  end
+end

metadata

@@ -0,0 +1,171 @@
+--- !ruby/object:Gem::Specification
+name: bio-jaspar
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Jessica Lee
+- Wasserman Lab
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-09-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: mysql2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.19
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.19
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  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: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.3
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  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: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.1
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+description: Basic tools for parsing, searching, and comparing JASPAR motifs; Based
+  on Bio.motifs module in Biopython
+email: 
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- lib/bio-jaspar.rb
+- lib/bio-jaspar/jaspar.rb
+- test/helper.rb
+- test/test_bio-jaspar.rb
+homepage: http://github.com/wassermanlab/jaspar-bioruby
+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: 2.4.6
+signing_key: 
+specification_version: 4
+summary: Tools for JASPAR motifs in BioRuby
+test_files: []