bio-polyploid-tools 1.0.0 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: b787eef663d8c1b2932b38a877bb870521e71c72f6584d9b08d3ebf0c937b36e
+  metadata.gz: a5d146ea101ef0f742e6e058708c01b938f2b296d4e8e2085577a2d9fc9f1d4c
+  data.tar.gz: f98358f44992285c58bf9be6c8774ee35da19066a96d3fe885901495129bb678
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+  data.tar.gz: 75af81e9a4f8207a4b47f414ff898dccd53c830a9d853dbe2a51bb86ecb074fe9ca29000ec99ce5a18e3ccfcf9be480eb92bdca392fa068168eba3824d6b5b71

data/VERSION

@@ -1 +1 @@
-1.0.0
+1.1.0

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[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 
@@ -136,6 +136,11 @@ OptionParser.new do |opts|
   opts.on("-H", "--max_hits INT", "Maximum number of hits to the reference. If there are more hits than this value, the marker is ignored") do |o|
     options[:max_hits] = o.to_i
   end
+
+  opts.on("-S", "--max_specific_primers INT", "Maximum number of candidate primers to attempt to design. Default: #{options[:max_specific_primers]} ") do |o|
+    options[:max_specific_primers]  = o.to_i
+  end
+  
 end.parse!
 
 
@@ -362,7 +367,7 @@ write_status "Running primer3"
 file = File.open(primer_3_input, "w")
 
 Bio::DB::Primer3.prepare_input_file(file, options[:primer_3_preferences])
-added_exons = container.print_primer_3_exons(file, nil, snp_in)
+added_exons = container.print_primer_3_exons(file, nil, snp_in,  max_specific_primers: options[:max_specific_primers] )
 file.close
 
 Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output}) if added_exons > 0

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 1.0.0 ruby lib
+# stub: bio-polyploid-tools 1.1.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "1.0.0"
+  s.version = "1.1.0"
 
   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 = "2019-07-05"
+  s.date = "2019-10-21"
   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/ExonContainer.rb

@@ -151,7 +151,7 @@ module Bio::PolyploidTools
       end
     end
 
-    def print_primer_3_exons (file, target_chromosome , parental )
+    def print_primer_3_exons (file, target_chromosome , parental,  max_specific_primers: 20 )
       added = 0
       
       @snp_map.each do | gene, snp_array|
@@ -159,7 +159,7 @@ module Bio::PolyploidTools
           string = ""
           begin 
             primer_3_min_seq_length
-            string = snp.primer_3_string( snp.chromosome, parental )
+            string = snp.primer_3_string( snp.chromosome, parental,  max_specific_primers: max_specific_primers )
             #TODO: add tan error to the SNP this snp has more than max_hits. 
             #Or maybe inside the SNP file. 
             if string.size > 0

data/lib/bio/PolyploidTools/SNP.rb

@@ -371,7 +371,7 @@ module Bio::PolyploidTools
     end
 
 
-    def primer_3_all_strings(target_chromosome, parental) 
+    def primer_3_all_strings(target_chromosome, parental, max_specific_primers: 20 ) 
 
       pr = primer_region(target_chromosome, parental )
       primer_3_propertes = Array.new
@@ -402,51 +402,52 @@ module Bio::PolyploidTools
       else
         @snp_type = "non-homoeologous"
       end
-
+      
       pr.chromosome_specific.each do |pos|
-
+        break if max_specific_primers <= 0
         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.almost_chromosome_specific.each do |pos|
-        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}
+      pr.crhomosome_specific_intron.each do |pos|
+        break if max_specific_primers <= 0
+        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_semispecific exon #{@snp_type} #{chromosome}"
+        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|
-
-        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}
+      pr.almost_chromosome_specific.each do |pos|
+        break if max_specific_primers <= 0
+        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_specific exon #{@snp_type} #{chromosome}"
+        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
         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}
       primer_3_propertes << return_primer_3_string(args)
       args[:name] = "#{gene}:#{original}#{position}#{snp} #{snp_in} chromosome_nonspecific all #{@snp_type} #{chromosome}"
       args[:sequence] = seq_snp
       primer_3_propertes << return_primer_3_string(args)
-
-
       primer_3_propertes
     end
 
@@ -458,8 +459,8 @@ module Bio::PolyploidTools
       "#{original}#{position}#{snp}".upcase
     end
 
-    def primer_3_string(target_chromosome, parental) 
-      strings = primer_3_all_strings(target_chromosome, parental) 
+    def primer_3_string(target_chromosome, parental, max_specific_primers: 20) 
+      strings = primer_3_all_strings(target_chromosome, parental, max_specific_primers: max_specific_primers) 
       strings.join
     end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.1.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-05 00:00:00.000000000 Z
+date: 2019-10-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio