bio-polyploid-tools 1.1.0 → 1.1.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a5d146ea101ef0f742e6e058708c01b938f2b296d4e8e2085577a2d9fc9f1d4c
-  data.tar.gz: f98358f44992285c58bf9be6c8774ee35da19066a96d3fe885901495129bb678
+  metadata.gz: 991c0406b74a17197e779e6a44f555b86c3e81eec2c32e029894d85774b691c1
+  data.tar.gz: 3e41e331a0b72a829f90c668594f241268fdcde0931a8ed38ceaff4a2ce6f580
 SHA512:
-  metadata.gz: d6d55c1f56bba647f010211cc7862ccd21faa012be8796babe58037ff7da6e434006d0184a9be6440f5a276c44b0699d30121b39ab42cc4cac62dd3ebc0f8d7b
-  data.tar.gz: 75af81e9a4f8207a4b47f414ff898dccd53c830a9d853dbe2a51bb86ecb074fe9ca29000ec99ce5a18e3ccfcf9be480eb92bdca392fa068168eba3824d6b5b71
+  metadata.gz: f6f7eb2032143ababc478e3713ae3c89fadea3457b441ff00c737f16bff8b4799f03ac7d836962a9d46ce89ddb88c0efb19f8936dda9c26234b63a353bf35670
+  data.tar.gz: d942ced9c2e1a31cca87b012b4a2a346f79a41c0cc39d66cfe14f5707bcd8824f8caf637bd9a35c966bfe6ddfedba1f75fec9418075bcc6b829b9601c5a9838a

data/VERSION

@@ -1 +1 @@
-1.1.0
+1.1.1

data/bin/polymarker.rb

@@ -41,7 +41,7 @@ options[:database]  = false
 options[:filter_best]  = false
 options[:aligner] = :blast
 options[:max_hits] = 8
-options[:max_specific_primers]  = 20
+options[:max_specific_primers]  = 15
 options[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 1.1.0 ruby lib
+# stub: bio-polyploid-tools 1.1.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "1.1.0"
+  s.version = "1.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
-  s.date = "2019-10-21"
+  s.date = "2019-11-03"
   s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
   s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
   s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "marker_to_vcf.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "polymarker_deletions.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze, "vcfToPolyMarker.rb".freeze]

data/lib/bio/PolyploidTools/SNP.rb

@@ -403,44 +403,47 @@ module Bio::PolyploidTools
         @snp_type = "non-homoeologous"
       end
       
+      total_candidates  = pr.chromosome_specific.size
+      total_candidates += pr.crhomosome_specific_intron.size 
+      total_candidates += pr.almost_chromosome_specific.size
+      total_candidates += pr.almost_crhomosome_specific_intron.size
+
+      skip_specific = total_candidates > max_specific_primers
+
       pr.chromosome_specific.each do |pos|
-        break if max_specific_primers <= 0
+        break if skip_specific
         args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_specific exon #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
         args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_specific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
-        max_specific_primers -= 1
       end
 
       pr.crhomosome_specific_intron.each do |pos|
-        break if max_specific_primers <= 0
+        break if skip_specific
         args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_specific intron #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
         args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_specific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
-        max_specific_primers -= 1
       end
 
       pr.almost_chromosome_specific.each do |pos|
-        break if max_specific_primers <= 0
+        break if skip_specific
         args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_semispecific exon #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
         args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_semispecific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
-        max_specific_primers -= 1
       end
 
       pr.almost_crhomosome_specific_intron.each do |pos|
-        break if max_specific_primers <= 0
+        break if skip_specific
         args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_semispecific intron #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}
         primer_3_propertes << return_primer_3_string(args)
         args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_semispecific exon #{@snp_type} #{chromosome}"
         args[:sequence] = seq_snp
         primer_3_propertes << return_primer_3_string(args)
-        max_specific_primers -= 1
       end
 
       args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_nonspecific all #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :sequence=>seq_original}

data/lib/bio/db/primer3.rb

@@ -30,7 +30,6 @@ module Bio::DB::Primer3
     opts.each do |key,value|
       file.puts "#{key.to_s.upcase}=#{value}\n"
     end
-    # file.puts "="
   end
 
   def self.run(opts={})

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 1.1.0
+  version: 1.1.1
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-10-21 00:00:00.000000000 Z
+date: 2019-11-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio