bio-pangenome 0.1.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 67ff78e3e817086eb54e9f3c2a93bad8dfec84733d2e6db2a1ccb716543ae3cb
+  data.tar.gz: b9720ab3108dba2864a2f94762597c3cb89fd0837e5853d6f08215abe9f8fce8
+SHA512:
+  metadata.gz: b1643aecb2e252b8c1cc4fe3328d9b296d9ac0f63987544b954320a720346b7175234d6a83c9322baac25f057edc171e530e11181714016aeca73d0da791a650
+  data.tar.gz: d34eafed8d0080ecfbdc68dad5a39366fb18fec2666337e69a00f656f9c2d187b7b9aad062eb3197c24f881194343ce87b4730caafb51d729a80b77722883bd3

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

@@ -0,0 +1,13 @@
+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

@@ -0,0 +1,15 @@
+source "https://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "bio"
+gem "bio-blastxmlparser"
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "simplecov", ">= 0"
+  gem "juwelier"
+  gem "bundler", ">= 1.0.21"
+end

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2019 homonecloco
+
+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 +1,47 @@
+# bio-pangenome
+
+[![Build Status](https://secure.travis-ci.org/homonecloco/bioruby-pangenome.png)](http://travis-ci.org/homonecloco/bioruby-pangenome)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-pangenome
+```
+
+## Usage
+
+```ruby
+require 'bio-pangenome'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/homonecloco/bioruby-pangenome
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-pangenome)
+
+## Copyright
+
+Copyright (c) 2019 homonecloco. See LICENSE.txt for further details.
+

data/README.rdoc

@@ -0,0 +1,48 @@
+= bio-pangenome
+
+{<img
+src="https://secure.travis-ci.org/homonecloco/bioruby-pangenome.png"
+/>}[http://travis-ci.org/#!/homonecloco/bioruby-pangenome]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-pangenome
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-pangenome'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/homonecloco/bioruby-pangenome
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-pangenome
+
+== Copyright
+
+Copyright (c) 2019 homonecloco. See LICENSE.txt for further details.
+

data/Rakefile

@@ -0,0 +1,52 @@
+# 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 'juwelier'
+Juwelier::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-pangenome"
+  gem.homepage = "http://github.com/Uauy-Lab/bioruby-pangenome"
+  gem.license = "MIT"
+  gem.summary = %Q{Scripts to analyse pangenomes.}
+  gem.description = %Q{Tools to find similarity between pangenomes.}
+  gem.email = "ricardo.ramirez-gonzalez@jic.ac.uk"
+  gem.authors = ["Ricardo H. Ramirez-Gonzalez"]
+  # dependencies defined in Gemfile
+end
+
+Juwelier::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+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-pangenome #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.1.1

data/bin/pangenome_blast_flanking.rb

@@ -0,0 +1,114 @@
+#!/usr/bin/env ruby
+#
+# BioRuby bio-pangenome Plugin BioPangenome
+# Author:: homonecloco
+# Copyright:: 2019
+
+USAGE = "panggenome_blast_flanking.rb [options]"
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+# print banner
+print "panggenome_blast_flanking #{version} by Ricardo H. Ramirez-Gonzalez 2019\n"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+path = gempath + '/lib/bio-pangenome.rb'
+require path
+#require 'bio-pangenome'
+require 'optparse'
+require 'tmpdir'
+
+options = { 
+  :transcript_mapping => "sorted_filtered_mapping.csv.gz",
+  :lines => "lines.txt",
+  :genes => "genes.txt",
+  :no_windows => 0, 
+  :window => 0,
+  :distance => 2000
+}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options]"
+
+  o.on('-t', '--transcript_mapping [sorted_filtered_mapping.csv.gz]', 'File with the  mappings across  transcriptomes') do |arg|
+    options[:transcript_mapping] = arg
+  end
+
+  o.on('-g','--genes [genes.txt]', 'File with the list of genes') do |arg|
+    options[:genes] = arg
+  end
+
+  o.on('-n','--no_windows INT', "Number of chunks to divide the genes list. 0 to not split") do |arg|
+    options[:no_windows] = arg.to_i
+  end
+
+  o.on('-w', "--window INT", "Current window to run") do |arg|
+    options[:window] = arg.to_i 
+  end
+
+  o.on('-d', "--distance DIST", "Name of the distance set. Ues 'cds' to align cds. default 2000") do |arg|
+    options[:distance] = arg
+  end
+
+  o.on("-b", "--basepath PATH", "Folder with the sequences and mapping positions across genomes") do |arg|
+    options[:basepath] = arg
+  end
+
+  o.on("-o", "--output PATH", "Folder with the output. If  there are chunks, they will be used") do |arg|
+    options[:output] = arg
+  end
+
+  o.on("-l", "--lines PATH", "File containing the lines to be analysed") do |arg|
+    options[:lines] = arg
+  end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+opts.parse!(ARGV)
+
+genes = BioPangenome.load_genes(options[:genes], window: options[:window], no_windows: options[:no_windows] )
+puts "Genes count: #{genes.size}"
+
+lines = BioPangenome.load_lines(options[:lines])
+
+projected_genes = BioPangenome.load_projected_genes options[:transcript_mapping], genes: genes
+
+variety_coordinates = BioPangenome.load_mapping_hash(
+  varieties:lines, 
+  genes: projected_genes ,
+  prefix: options[:basepath],
+  distance: options[:distance]
+  )
+
+seqs = BioPangenome.load_sequences_from_hash(
+  coordinates:variety_coordinates,
+  prefix: options[:basepath],
+  distance: options[:distance],
+  projected_genes: projected_genes
+  )
+
+output = options[:output].to_s
+output = output + "_" + options[:window].to_s if options[:no_windows] > 0
+
+Dir.mktmpdir do |temp_dir|
+  puts "Aligning in  #{temp_dir}"
+  BioPangenome.align_gene_groups(
+    seqs: seqs, 
+    distance:options[:distance],
+    output: output,
+    tmp_folder: temp_dir)
+end
+
+
+
+

data/lib/bio-pangenome.rb

@@ -0,0 +1,12 @@
+# 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-pangenome/pangenome.rb'
+

data/lib/bio-pangenome/pangenome.rb

@@ -0,0 +1,201 @@
+
+require 'zlib'
+require 'bio'
+require 'csv'
+require 'set'
+require 'bio-blastxmlparser'
+
+module BioPangenome
+	Transcript = Struct.new(:id, :gene, :chromosome,:version,:count,:transcript,:confidence, :count_int, :isoform)
+	GeneFlankingRegion = Struct.new(:transcript, :gene, :ann, :region, :id, :flank_length, :sequence, :line)
+
+	def self.parseTranscript name
+		arr=name.split(".")
+		match = /TraesCS(?<chr>[[:alnum:]]{1,2})(?<ver>[[:digit:]]{2})G(?<count>[[:digit:]]+)(?<conf>[[:upper:]]*)/.match arr[0]
+		raise "Unable to parse: #{name}" unless match
+		Transcript.new(name, arr[0],match[:chr],match[:ver],match[:count],arr[1],match[:conf], match[:count].to_i, arr[1])
+	end
+	def self.parseEITranscript name
+		arr=name.split(".")
+		match = /Traes(?<chr>[[:upper:]]{3}_scaffold_[[:digit:]]*)_(?<ver>[[:digit:]]{2})G(?<count>[[:digit:]]+)(?<conf>[[:upper:]]*)/.match arr[0]
+		raise "Unable to parse: #{name}" unless match
+		Transcript.new(name, arr[0],match[:chr].downcase,match[:ver],match[:count],arr[1],match[:conf], match[:count].to_i, arr[1])
+	end
+
+	def self.parsePGSBTranscript name
+		arr=name.split(".")
+		match = /Traes(?<variety>[[:upper:]]{3})(?<chr>[[:alnum:]]{1,2})(?<ver>[[:digit:]]{2})G(?<count>[[:digit:]]+)(?<conf>[[:upper:]]*)/.match arr[0]
+
+		raise "Unable to parse: #{name}" unless match
+		Transcript.new(name, arr[0],match[:chr],match[:ver],match[:count],match[:variety], match[:conf],match[:count].to_i, arr[1])
+	end
+	def self.parseSequenceName region, name
+		match = /(?<transcript>[[:alnum:]].+)_(?<ann>.+)_(?<flank_length>[[:digit:]]+bp)/.match name
+		arr2=match[:transcript].split "."
+		GeneFlankingRegion.new(match[:transcript],arr2[0],match[:ann], region, name, match[:flank_length] , nil, nil)
+	end
+
+	def self.load_mapping_hash(varieties:[],  transcripts:[], genes:[], distance: 1000, prefix: "../flanking/releasePGSBV1/",  suffix: ".RefSeqv1.1")
+		ret = Hash.new { |h, k| h[k] = Hash.new }
+		varieties.each do |v|
+			path = "#{prefix}#{distance}bp/#{v}_#{distance}bp_#{suffix}.reg.map"
+			$stderr.puts path
+			File.foreach(path) do |line|
+				line.chomp!
+				arr = line.split("\t")
+				begin
+					parsed = parseSequenceName(arr[0], arr[1])
+				rescue Exception => e
+					throw "Unable to parse #{line} (#{v}) [#{e.to_s}]" 
+				end
+				next unless transcripts.include? parsed.transcript or genes.include? parsed.gene
+				ret[v][parsed.region] = parsed
+			end
+		end
+		ret
+	end
+
+	def self.blast_pair_fast(path_a, path_b, out_path, program: "blastn")
+		cmd = "#{program} -query #{path_a} -subject #{path_b} -task #{program} -out #{out_path} -outfmt '5' "
+		system cmd
+		n = Bio::BlastXMLParser::XmlIterator.new(out_path).to_enum
+		max_length = 0
+		max_pident = 0.0
+		n.each do | iter |
+			iter.each do | hit |
+				hit.each do | hsp |
+					if hsp.align_len > max_length
+						max_length = hsp.align_len
+						max_pident = 100 * hsp.identity.to_f / hsp.align_len.to_f
+					end
+				end
+			end
+		end
+		[max_length, max_pident]
+	end
+
+
+	def self.load_sequences_from_hash(coordinates:{},  prefix: "../flanking/filtered/",  suffix: "RefSeqv1.1", distance: 1000, projected_genes: {})
+		ret = Hash.new { |h, k| h[k] = Hash.new }
+		coordinates.each_pair do |variety, coords|
+
+			path = "#{prefix}/#{distance}bp/#{variety}_#{distance}bp_#{suffix}.fa.gz"
+			puts "Loading: #{path}"
+			infile = open(path)
+			io = Zlib::GzipReader.new(infile) 
+			Bio::FlatFile.open(Bio::FastaFormat, io) do |fasta_file|
+				fasta_file.each do |entry|
+					next unless coords[entry.definition]
+					seq_name = coords[entry.definition]
+					seq = entry.seq
+					seq.gsub!(/N*$/, '')
+					seq.gsub!(/^N*/, '')
+					seq_name.sequence = seq
+					base_gene = projected_genes[seq_name.gene]["gene"]
+					ret[base_gene][variety] = seq_name unless ret[base_gene][variety]
+				end
+			end
+			io.close
+		end
+		ret
+	end
+
+	def self.align_gene_groups( seqs:{}, tmp_folder:"/Volumes/PanGenome/GeneRegions/201910_v2_v3/tmp", output:"../pairwise_blast_oct_2019/varieties_6A_identites", distance: 0 )
+		out_tmp="#{tmp_folder}/out.blast"
+		FileUtils.mkdir_p(tmp_folder)
+		out = File.open("#{output}_#{distance}bp.tab", "w")
+		out.puts [ "transcript" , "query", "subject" ,  "var_query", "var_subject", "aln_type", "length" , "pident" , "Ns_query", "Ns_subject", "Ns_total", "Flanking"   ].join("\t")
+		seqs.each_pair do |transcript, transcript_seqs|
+			vars = transcript_seqs.keys
+			vars_done = []
+			ns = {}
+			vars.each do |v1|
+				tmp =  tmp_folder  + "/" + v1 + ".fa"
+				s = transcript_seqs[v1]
+				seq = ">#{s.id}\n#{s.sequence}"
+				File.open(tmp, 'w') {|f| f.write(seq) }
+				ns[v1] = s.sequence.count('Nn')
+			end
+			vars.each do |v1|
+				tmp1 =  tmp_folder  + "/" + v1 + ".fa"
+				s1 = transcript_seqs[v1]
+				next unless s1.sequence.length > 0
+				vars.each do |v2|
+					next if v1 == v2
+					next if vars_done.include? v2
+					s2 = transcript_seqs[v2]
+					next unless s2.sequence.length > 0
+					tmp2 =  tmp_folder  + "/" + v2 + ".fa"
+					to_print = [transcript, s1.id , s2.id , v1,v2,"#{v1}->#{v2}"]
+					to_print << blast_pair_fast(tmp1, tmp2, out_tmp) 
+					to_print << ns[v1] 
+					to_print << ns[v2]
+					to_print << ns[v1] + ns[v2]
+					to_print << distance
+					out.puts to_print.join("\t")
+				end
+				vars_done << v1
+			end
+		end
+		out.close
+	end
+
+	def self.load_cds_sequences( varieties:[], genes:{}, prefix: "../flanking/filtered/",  suffix: ".cds.fa.gz", set_id: "cds" )
+		ret = Hash.new { |h, k| h[k] = Hash.new }
+		varieties.each do |variety|
+			path = "#{prefix}/#{variety}#{suffix}"
+			infile = open(path)
+			io = Zlib::GzipReader.new(infile) 
+			Bio::FlatFile.open(Bio::FastaFormat, io) do |fasta_file|
+				fasta_file.each do |entry|
+					arr = entry.definition.split(".")
+					next unless genes[arr[0]]
+					row = genes[arr[0]]
+					seq_name = GeneFlankingRegion.new(entry.definition,
+						row["gene"], "",
+						"", entry.definition, set_id, nil, variety )
+					seq = entry.seq
+					seq.gsub!(/N*$/, '')
+					seq.gsub!(/^N*/, '')
+					seq_name.sequence = seq
+					base_gene = seq_name.gene
+					ret[base_gene][variety] = seq_name unless ret[base_gene][variety]
+				end
+			end
+			io.close
+		end
+		ret
+	end
+
+	def self.load_projected_genes(transcript_mapping, genes:[])
+		projected_genes = {}
+		Zlib::GzipReader.open(transcript_mapping) do |gzip|
+			csv = CSV.new(gzip, headers: true)
+			csv.each do |row|
+				next unless genes.include? row["gene"]
+				projected_genes[row["projected_gene"]] = row
+			end
+		end
+		projected_genes
+	end
+
+	def self.load_genes(filename, window: 0, no_windows: 0)
+		genes = File.readlines(filename).map do |t|
+			t.chomp!.split(".")[0]
+		end
+		if no_windows > 0
+			puts "'loading window #{window} of #{no_windows}'"
+			window_size = genes.size/no_windows
+			start = window * window_size
+			genes = genes[start, window_size]
+		end
+		genes
+	end
+
+	def self.load_lines(filename)
+		File.readlines(filename).map do |t|
+			t.chomp!.rstrip
+		end
+	end
+
+end

data/test/helper.rb

@@ -0,0 +1,34 @@
+require 'simplecov'
+
+module SimpleCov::Configuration
+  def clean_filters
+    @filters = []
+  end
+end
+
+SimpleCov.configure do
+  clean_filters
+  load_adapter 'test_frameworks'
+end
+
+ENV["COVERAGE"] && SimpleCov.start do
+  add_filter "/.rvm/"
+end
+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-pangenome'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-pangenome.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioPangenome < 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"
+  end
+end

metadata

@@ -0,0 +1,157 @@
+--- !ruby/object:Gem::Specification
+name: bio-pangenome
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- Ricardo H. Ramirez-Gonzalez
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2019-11-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  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'
+- !ruby/object:Gem::Dependency
+  name: bio-blastxmlparser
+  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'
+- !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: 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: simplecov
+  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: juwelier
+  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: 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: Tools to find similarity between pangenomes.
+email: ricardo.ramirez-gonzalez@jic.ac.uk
+executables:
+- pangenome_blast_flanking.rb
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/pangenome_blast_flanking.rb
+- lib/bio-pangenome.rb
+- lib/bio-pangenome/pangenome.rb
+- test/helper.rb
+- test/test_bio-pangenome.rb
+homepage: http://github.com/Uauy-Lab/bioruby-pangenome
+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: []
+rubygems_version: 3.0.6
+signing_key: 
+specification_version: 4
+summary: Scripts to analyse pangenomes.
+test_files: []