bio-polyploid-tools 0.5.1 → 0.5.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: b25e3a15320a41139d95e0dc4b5807d076276429
+  metadata.gz: 23c185fa7183010bca4c619fa252ecd2d58e2d13
+  data.tar.gz: a093ad10be19c610df004bc2b0ad8834dcd7ca00
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+  data.tar.gz: 4941e7ca5027e0fed010dcd6523f82fafc1a8db75a9826f4c14f6fef20a54e79f614d91560cf398174e23ebbe1f2c71b80916ba118ae28ed50fe4a451f3c8410

data/VERSION

@@ -1 +1 @@
-0.5.1
+0.5.2

data/bin/polymarker.rb

@@ -79,8 +79,9 @@ OptionParser.new do |opts|
   
   opts.on("-p", "--primer_3_preferences FILE", "file with preferences to be sent to primer3") do |o|
     options[:primer_3_preferences] = Bio::DB::Primer3.read_primer_preferences(o, options[:primer_3_preferences] )
-
   end
+
+  
     
 end.parse!
 

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.5.1 ruby lib
+# stub: bio-polyploid-tools 0.5.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.5.1"
+  s.version = "0.5.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez"]
-  s.date = "2014-10-14"
+  s.date = "2014-10-28"
   s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat"
   s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
   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"]

data/lib/bio/PolyploidTools/PrimerRegion.rb

@@ -1,6 +1,6 @@
 module Bio::PolyploidTools
   class PrimerRegion
-    attr_accessor :snp_pos, :sequence, :chromosome_specific, :almost_chromosome_specific, :crhomosome_specific_intron , :almost_crhomosome_specific_intron, :homeologous
+    attr_accessor :snp_pos, :sequence, :chromosome_specific, :almost_chromosome_specific, :crhomosome_specific_intron , :almost_crhomosome_specific_intron, :homoeologous
 
     def initialize
 

data/lib/bio/PolyploidTools/SNP.rb

@@ -203,11 +203,11 @@ module Bio::PolyploidTools
           when mask[i] == '&'
             #This is the SNP we take the parental
             pr.snp_pos = position_in_region
-            pr.homeologous = false
+            pr.homoeologous = false
           when mask[i] == ':'
             #This is the SNP we take the parental
             pr.snp_pos = position_in_region
-            pr.homeologous = true
+            pr.homoeologous = true
           when mask[i] == '-'
             #When the mask doesnt detect a SNP, so we take the parental
             parental[i] = chromosome_seq[i] unless Bio::NucleicAcid::is_unambiguous(parental[i])
@@ -304,10 +304,10 @@ module Bio::PolyploidTools
 
       rev_pos = seq_snp.size - position
 
-      if pr.homeologous
-        snp_type = "homeologous"
+      if pr.homoeologous
+        snp_type = "homoeologous"
       else
-        snp_type = "non-homeologous"
+        snp_type = "non-homoeologous"
       end
 
       pr.chromosome_specific.each do |pos|

data/lib/bio/db/primer3.rb

@@ -471,10 +471,10 @@ module Bio::DB::Primer3
         @exon = false
       end
 
-      if @polymorphism.to_sym == :homeologous
-        @homeologous = true
+      if @polymorphism.to_sym == :homoeologous
+        @homoeologous = true
       else
-        @homeologous = false
+        @homoeologous = false
       end
       @parsed = true
       @orientation = @orientation.to_sym
@@ -492,10 +492,10 @@ module Bio::DB::Primer3
       @chromosome
     end
     
-    def homeologous?
-      return @homeologous if @parsed
+    def homoeologous?
+      return @homoeologous if @parsed
       parse_header
-      @homeologous
+      @homoeologous
     end
 
     def type

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.5.1
+  version: 0.5.2
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-14 00:00:00.000000000 Z
+date: 2014-10-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio