bio-polyploid-tools 0.4.0 → 0.4.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 612c7e5e39e8908003387efe2e6ba739b7fb981d
-  data.tar.gz: eac406e26c6985115884ba53f0c3dadf22bf3e81
+  metadata.gz: 8d839159cd2b8aee7e5586e5b04a4fadc1415b90
+  data.tar.gz: 30af7856bfe87e382b0e0e8c8890507b743d8057
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+  data.tar.gz: 80bdd7c718ab9c05155b8da99cec7ed543e938a942591acd0a53fce8cbe7e797ffb044e48b96734c795a5a9cda8b5cdd269d019766dffa0c5f498207744f9ef9

data/VERSION

@@ -1 +1 @@
-0.4.0
+0.4.1

data/bin/polymarker.rb

@@ -266,10 +266,10 @@ file = File.open(primer_3_input, "w")
 #file.puts("PRIMER_THERMODYNAMIC_PARAMETERS_PATH=#{primer_3_config}/")
 
 Bio::DB::Primer3.prepare_input_file(file, options[:primer_3_preferences])
-container.print_primer_3_exons(file, nil, snp_in)
+added_exons = container.print_primer_3_exons(file, nil, snp_in)
 file.close
 
-Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output})
+Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output}) if added_exons > 0
 
 
 #5. Pick the best primer and make the primer3 output
@@ -282,7 +282,7 @@ snps.each do |snp|
   kasp_container.add_snp(snp) 
 end
 
-kasp_container.add_primers_file(primer_3_output)
+kasp_container.add_primers_file(primer_3_output) if added_exons > 0
 header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{snp_in},#{original_name},common,primer_type,orientation,#{snp_in}_TM,#{original_name}_TM,common_TM,selected_from,product_size"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
 

data/bin/snp_position_to_polymarker.rb

@@ -37,7 +37,9 @@ OptionParser.new do |opts|
   opts.on("-o", "--out CSV", "Output file ") do |o|
     options[:output] = o
   end
-  opts.on()("-f", "--flanking_size INT", "Flanking size around the SNP")
+  opts.on("-f", "--flanking_size INT", "Flanking size around the SNP") do |o|
+    options[:flanking_size] = o.to_i
+  end
   
 end.parse!
 #reference="/Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa"

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 0.4.0 ruby lib
+# stub: bio-polyploid-tools 0.4.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.4.0"
+  s.version = "0.4.1"
 
   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 = "2014-09-25"
+  s.date = "2014-09-26"
   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/BIOExtensions.rb

@@ -59,4 +59,6 @@ class Hash
   def join(keyvaldelim=$,, entrydelim=$,)
     map {|e| e.join(keyvaldelim) }.join(entrydelim)
   end
-end
+end
+
+

data/lib/bio/PolyploidTools/ExonContainer.rb

@@ -5,7 +5,7 @@ module Bio::PolyploidTools
     attr_reader :parental_1_name, :parental_2_name, :gene_models_db
     attr_reader :chromosomes, :snp_map
     attr_reader :parents
-    attr_accessor :flanking_size
+    attr_accessor :flanking_size , :primer_3_min_seq_length
 
     BASES = [:A, :C, :G, :T]
     #Sets the reference file for the gene models
@@ -14,6 +14,7 @@ module Bio::PolyploidTools
       @parents=Hash.new
       @snp_map = Hash.new 
       @snp_contigs
+      @primer_3_min_seq_length = 50
     end
 
     def gene_models(path)
@@ -126,17 +127,24 @@ module Bio::PolyploidTools
     end
 
     def print_primer_3_exons (file, target_chromosome , parental )
+      added = 0
       @snp_map.each do | gene, snp_array|
         snp_array.each do |snp|
+          string = ""
           begin 
-          string = snp.primer_3_string( snp.chromosome, parental )
-          file.puts string if string.size > 0
+            primer_3_min_seq_length
+            string = snp.primer_3_string( snp.chromosome, parental )
+            if string.size > 0
+              file.puts string
+              added += 1
+            end 
            rescue Exception=>e
              @missing_exons << snp.to_s
               #$stderr.puts e.to_s
             end
         end 
       end
+      return added
     end
 
     def add_alignments(opts=Hash.new) 

data/lib/bio/PolyploidTools/SNP.rb

@@ -12,7 +12,7 @@ module Bio::PolyploidTools
     attr_accessor :template_sequence
     attr_accessor :use_reference
     attr_accessor :genomes_count
-    
+    attr_accessor :primer_3_min_seq_length 
     attr_accessor :chromosome
 
     #Format: 
@@ -35,13 +35,18 @@ module Bio::PolyploidTools
     end
 
     def initialize
-       @genomes_count = 3 #TODO: if we want to use this with other polyploids, me need to set this as a variable in the main script. 
+      @genomes_count = 3 #TODO: if we want to use this with other polyploids, me need to set this as a variable in the main script. 
+      @primer_3_min_seq_length = 50
     end
 
-    def to_polymarker_sequence
+    def to_polymarker_sequence(flanking_size)
       out = template_sequence.clone
       out[position-1]  = "[#{original}/#{snp}]"
-      out
+
+      start = position - flanking_size - 1
+      start = 0 if start < 0
+      total = flanking_size * 2 + 6
+      out[start , total ]
     end
     
     def snp_id_in_seq
@@ -283,6 +288,8 @@ module Bio::PolyploidTools
       primer_3_propertes = Array.new
 
       seq_original = String.new(pr.sequence)
+      put seq_original.size << "-" << primer_3_min_seq_length
+      return primer_3_propertes if seq_original.size < primer_3_min_seq_length
       seq_original[pr.snp_pos] = self.original
       seq_original_reverse = reverse_complement_string(seq_original)
 
@@ -407,16 +414,10 @@ module Bio::PolyploidTools
               seq[local_pos_in_gene] = self.original 
             end
         end
-        #puts "local_pos_in_gene #{local_pos_in_gene}"
-        #puts "'#{name}' compared to '#{self.snp_in}'"
-        #puts seq
         seq[local_pos_in_gene] = seq[local_pos_in_gene].upcase
         seq[local_pos_in_gene] = self.snp if name == self.snp_in  
-        #puts seq
-        #puts "__"
         @surrounding_parental_sequences [name] = cut_and_pad_sequence_to_primer_region(seq)
       end
-     # puts "&&&&\n#{surrounding_parental_sequences['A']}\n#{surrounding_parental_sequences['B']}\n&&&&"
       @surrounding_parental_sequences
     end
 
@@ -430,7 +431,6 @@ module Bio::PolyploidTools
     end
 
     def cut_and_pad_sequence_to_primer_region(sequence)
-     # p "cut_and_pad_sequence_to_primer_region #{local_position} #{flanking_size}" 
       ideal_min = self.local_position - flanking_size 
       ideal_max = self.local_position + flanking_size
       left_pad = 0
@@ -448,10 +448,7 @@ module Bio::PolyploidTools
     end
 
     def sequences_to_align
-       p @sequences_to_align.inspect
       @sequences_to_align = surrounding_parental_sequences.merge(surrounding_exon_sequences) unless @sequences_to_align
-    #  p "sequences_to_align"
-     
       @sequences_to_align
     end
 

data/lib/bio/PolyploidTools/SNPSequence.rb

@@ -44,6 +44,7 @@ module Bio::PolyploidTools
       @position = Regexp.last_match(:pre).size + 1
       @original = Regexp.last_match(:org)
       @snp = Regexp.last_match(:snp)
+      
       amb_base = Bio::NucleicAcid.to_IUAPC("#{@original}#{@snp}")
       
       @template_sequence = "#{Regexp.last_match(:pre)}#{amb_base}#{Regexp.last_match(:pos)}"

data/lib/bio/db/exonerate.rb

@@ -199,9 +199,7 @@ module Bio::DB::Exonerate
       reg.start = target_snp_pos - flanking_size
       reg.end = target_snp_pos + flanking_size
       raise  ExonerateException.new "Target Query out of bounds!" unless position.between?(query_start, query_end)
-      #puts "Flanking region for #{position} in exon between ( #{query_id}:#{query_start}-#{query_end}), the target in #{target_snp_pos} ( #{target_id}:#{target_start}-#{target_end}) "
-
-
+    
       reg
     end
 
@@ -226,7 +224,6 @@ module Bio::DB::Exonerate
       end
       #THis is in case the position is on a gap. 
       if @target_length == 0 and label == :G
-        #puts "Returning nil"
         @snp_in_gap = true
         ret = target_start
       end

data/lib/bio/db/primer3.rb

@@ -17,12 +17,6 @@ module Bio::DB::Primer3
   end
 
   def self.prepare_input_file(file, opts2={})
-    #file.puts("PRIMER_PRODUCT_SIZE_RANGE=50-150")
-#file.puts("PRIMER_MAX_SIZE=25")
-#file.puts("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1")
-#file.puts("PRIMER_LIBERAL_BASE=1")
-#file.puts("PRIMER_NUM_RETURN=5")
-#file.puts("PRIMER_THERMODYNAMIC_PARAMETERS_PATH=#{primer_3_config}/")
      opts = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.1
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-09-25 00:00:00.000000000 Z
+date: 2014-09-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio