bio-polyploid-tools 0.5.1 → 0.5.2

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checksums.yaml CHANGED
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.5.1
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+ 0.5.2
@@ -79,8 +79,9 @@ OptionParser.new do |opts|
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  opts.on("-p", "--primer_3_preferences FILE", "file with preferences to be sent to primer3") do |o|
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  options[:primer_3_preferences] = Bio::DB::Primer3.read_primer_preferences(o, options[:primer_3_preferences] )
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-
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  end
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+
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+
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  end.parse!
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@@ -2,16 +2,16 @@
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  # DO NOT EDIT THIS FILE DIRECTLY
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  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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- # stub: bio-polyploid-tools 0.5.1 ruby lib
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+ # stub: bio-polyploid-tools 0.5.2 ruby lib
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  Gem::Specification.new do |s|
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  s.name = "bio-polyploid-tools"
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- s.version = "0.5.1"
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+ s.version = "0.5.2"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.require_paths = ["lib"]
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  s.authors = ["Ricardo H. Ramirez-Gonzalez"]
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- s.date = "2014-10-14"
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+ s.date = "2014-10-28"
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  s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat"
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  s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
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  s.executables = ["bfr.rb", "count_variations.rb", "filter_blat_by_target_coverage.rb", "find_best_blat_hit.rb", "find_best_exonerate.rb", "hexaploid_primers.rb", "homokaryot_primers.rb", "map_markers_to_contigs.rb", "markers_in_region.rb", "polymarker.rb", "snp_position_to_polymarker.rb", "snps_between_bams.rb"]
@@ -1,6 +1,6 @@
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  module Bio::PolyploidTools
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  class PrimerRegion
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- attr_accessor :snp_pos, :sequence, :chromosome_specific, :almost_chromosome_specific, :crhomosome_specific_intron , :almost_crhomosome_specific_intron, :homeologous
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+ attr_accessor :snp_pos, :sequence, :chromosome_specific, :almost_chromosome_specific, :crhomosome_specific_intron , :almost_crhomosome_specific_intron, :homoeologous
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  def initialize
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@@ -203,11 +203,11 @@ module Bio::PolyploidTools
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  when mask[i] == '&'
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  #This is the SNP we take the parental
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  pr.snp_pos = position_in_region
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- pr.homeologous = false
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+ pr.homoeologous = false
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  when mask[i] == ':'
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  #This is the SNP we take the parental
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  pr.snp_pos = position_in_region
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- pr.homeologous = true
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+ pr.homoeologous = true
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  when mask[i] == '-'
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  #When the mask doesnt detect a SNP, so we take the parental
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  parental[i] = chromosome_seq[i] unless Bio::NucleicAcid::is_unambiguous(parental[i])
@@ -304,10 +304,10 @@ module Bio::PolyploidTools
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  rev_pos = seq_snp.size - position
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- if pr.homeologous
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- snp_type = "homeologous"
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+ if pr.homoeologous
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+ snp_type = "homoeologous"
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  else
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- snp_type = "non-homeologous"
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+ snp_type = "non-homoeologous"
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  end
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  pr.chromosome_specific.each do |pos|
@@ -471,10 +471,10 @@ module Bio::DB::Primer3
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  @exon = false
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  end
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- if @polymorphism.to_sym == :homeologous
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- @homeologous = true
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+ if @polymorphism.to_sym == :homoeologous
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+ @homoeologous = true
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  else
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- @homeologous = false
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+ @homoeologous = false
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  end
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  @parsed = true
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  @orientation = @orientation.to_sym
@@ -492,10 +492,10 @@ module Bio::DB::Primer3
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  @chromosome
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  end
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- def homeologous?
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- return @homeologous if @parsed
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+ def homoeologous?
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+ return @homoeologous if @parsed
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  parse_header
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- @homeologous
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+ @homoeologous
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  end
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  def type
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-polyploid-tools
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  version: !ruby/object:Gem::Version
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- version: 0.5.1
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+ version: 0.5.2
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  platform: ruby
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  authors:
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  - Ricardo H. Ramirez-Gonzalez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-10-14 00:00:00.000000000 Z
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+ date: 2014-10-28 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio