bio-polyploid-tools 0.5.1 → 0.5.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bin/polymarker.rb +2 -1
- data/bio-polyploid-tools.gemspec +3 -3
- data/lib/bio/PolyploidTools/PrimerRegion.rb +1 -1
- data/lib/bio/PolyploidTools/SNP.rb +5 -5
- data/lib/bio/db/primer3.rb +6 -6
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 23c185fa7183010bca4c619fa252ecd2d58e2d13
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data.tar.gz: a093ad10be19c610df004bc2b0ad8834dcd7ca00
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 7b6838728afb273a71afc44bfe790c947662c0d432229e3d40f7dca34e67928a849a95c9f52c90562b509e3ef1aa9d51147c7c60de49573baf826695cc425365
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data.tar.gz: 4941e7ca5027e0fed010dcd6523f82fafc1a8db75a9826f4c14f6fef20a54e79f614d91560cf398174e23ebbe1f2c71b80916ba118ae28ed50fe4a451f3c8410
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data/VERSION
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@@ -1 +1 @@
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1
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0.5.
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0.5.2
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data/bin/polymarker.rb
CHANGED
@@ -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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end
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end.parse!
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data/bio-polyploid-tools.gemspec
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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.
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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.
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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-
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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"]
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@@ -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, :
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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.
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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.
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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])
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@@ -304,10 +304,10 @@ module Bio::PolyploidTools
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rev_pos = seq_snp.size - position
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if pr.
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snp_type = "
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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-
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snp_type = "non-homoeologous"
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end
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pr.chromosome_specific.each do |pos|
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data/lib/bio/db/primer3.rb
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@@ -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 == :
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@
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if @polymorphism.to_sym == :homoeologous
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@homoeologous = true
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else
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@
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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
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@@ -492,10 +492,10 @@ module Bio::DB::Primer3
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@chromosome
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end
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def
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return @
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def homoeologous?
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return @homoeologous if @parsed
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parse_header
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@
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@homoeologous
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end
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def type
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metadata
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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.
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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-
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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
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