bio-polyploid-tools 0.4.5 → 0.4.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 9e11509fcfcbe8aa33caccd377dd0eca756713ef
-  data.tar.gz: ee00b6ac0ca58b233e3154caf2cc3e00b909a869
+  metadata.gz: 8560331ced4feb75e55252375e8ba98465afc5cf
+  data.tar.gz: 80ae4e52cf6612f7715316176763c17489afa8b7
 SHA512:
-  metadata.gz: 50afb04d54bd58599d730cfe44bcf7f8e51ec2aea62af870ebca9af0e685fc7a68e06da8a82b82973f1f8dcd6cb3f3414b1b93753dd64e37b19d12473b46adc1
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+  metadata.gz: 736c33a7fca6ea11d1456efe2967e237f39b3ecaa850ea04e2720254ba0fe74ee57f611872dcd31a37b58dfae69f6a0d76466080bf1e0296928e8b7d9b0d25b6
+  data.tar.gz: 3b5b6743f098b918d0b2336db079cf7b23be51690bdbf4e7531f4f27f716af1c143dabf11622692f7388e7742dbd92fb704646f8a143af46005225a5bceb263f

data/VERSION

@@ -1 +1 @@
-0.4.5
+0.4.6

data/bin/homokaryot_primers.rb

@@ -21,14 +21,22 @@ class HomokaryotContainer < Bio::PolyploidTools::ExonContainer
     flanking_size = 100
      File.open(filename) do | f |
        f.each_line do | line |
+        if ARGV.size == 1 #List with Sequence
+        snp = Bio::PolyploidTools::SNPSequence.parse(line)  
+        snp.use_reference = false
+        elsif ARGV.size == 2 #List and fasta file
          snp = Bio::PolyploidTools::SNP.parse(line)
+         snp.use_reference = true
+        end
+         #snp = Bio::PolyploidTools::SNP.parse(line)
+        # puts snp.gene
          snp.flanking_size = flanking_size
          if snp.position > 0
            snp.container = self
            snp.chromosome = chromosome
            snp.snp_in = snp_in
            snp.original_name = original_name
-           snp.use_reference = true
+           
            snp.container = self
            @snp_map[snp.gene] = Array.new unless   @snp_map[snp.gene] 
            @snp_map[snp.gene] << snp   
@@ -95,6 +103,7 @@ File.open(snp_file) do | f |
     snp = nil
     if ARGV.size == 1 #List with Sequence
       snp = Bio::PolyploidTools::SNPSequence.parse(line)  
+
     elsif ARGV.size == 2 #List and fasta file
       snp = Bio::PolyploidTools::SNP.parse(line)
       region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
@@ -112,13 +121,32 @@ File.open(snp_file) do | f |
 end
 
 
+output_folder="#{snp_file}_primer_design_#{Time.now.strftime('%Y%m%d-%H%M%S')}/"
+Dir.mkdir(output_folder)
+seqs_file= output_folder + "sequences.fa"
+written_seqs = Set.new
+reference_file = seqs_file unless reference_file
+  
+
+file = File.open(seqs_file, "w")
+snps.each do |snp|
+  unless written_seqs.include?(snp.gene)
+    written_seqs << snp.gene 
+    file.puts snp.to_fasta
+  end
+end
+file.close
+
+
 container = HomokaryotContainer.new
 container.add_parental({:name=>snp_in})
 container.add_parental({:name=>original_name})
-container.gene_models(reference_file)
+container.gene_models(reference_file) if reference_file
+
+
+
+
 
-output_folder="#{snp_file}_primer_design_#{Time.now.strftime('%Y%m%d-%H%M%S')}/"
-Dir.mkdir(output_folder)
 primer_3_input="#{output_folder}primer_3_input_temp"
 primer_3_output="#{output_folder}primer_3_output_temp"
 container.add_snp_file(snp_file, "PST130",  snp_in, original_name)

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 0.4.5 ruby lib
+# stub: bio-polyploid-tools 0.4.6 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.4.5"
+  s.version = "0.4.6"
 
   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 = "2014-10-04"
+  s.date = "2014-10-08"
   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/ExonContainer.rb

@@ -24,6 +24,7 @@ module Bio::PolyploidTools
 
     #Returns the sequence for a region in the gene models (exon)
     def gene_model_sequence(region)
+      #puts region
       seq=@gene_models_db.fetch_sequence(region)
 
 

data/lib/bio/PolyploidTools/SNP.rb

@@ -99,8 +99,12 @@ module Bio::PolyploidTools
       max = @position
      # puts "Calculating covered region for #{self.inspect}"
     #  puts "#{@exon_list.inspect}"
-      raise SNPException.new "Exons haven't been loaded for #{self.to_s}" if @exon_list.size == 0
-      
+      #raise SNPException.new "Exons haven't been loaded for #{self.to_s}" if @exon_list.size == 0
+      if @exon_list.size == 0
+        min = self.position - self.flanking_size
+        min = 1 if min < 1
+        max =  self.position + self.flanking_size
+      end
       @exon_list.each do | chromosome, exon |
        # puts exon.inspect
         reg = exon.query_region

data/lib/bio/db/primer3.rb

@@ -287,11 +287,11 @@ module Bio::DB::Primer3
 
       if  primer3record.primer_left_num_returned.to_i > 0 
         case
-        when primer3record.line == @line_2
+        when primer3record.line == @line_1
           primers_line_1 << primer3record
           #puts primer3record.inspect
           @primer3_line_1 = primer3record if not @primer3_line_1  or @primer3_line_1 > primer3record
-        when primer3record.line == @line_1
+        when primer3record.line == @line_2
           primers_line_2 << primer3record
           @primer3_line_2 = primer3record if not @primer3_line_2 or @primer3_line_2 > primer3record
         else
@@ -309,12 +309,12 @@ module Bio::DB::Primer3
 
     def best_pair
       return @best_pair if @best_pair
-      #@best_pair = nil
-      #@primerPairs.each do | primer |
-      #  @best_pair = primer if @best_pair == nil
-      #  @best_pair = primer if primer.size < @best_pair.size
-      #end
-      @best_pair = @primerPairs.first
+      @best_pair = nil
+      @primerPairs.each do | primer |
+        @best_pair = primer if @best_pair == nil
+        @best_pair = primer if primer.size < @best_pair.size
+      end
+      #@best_pair = @primerPairs.min
       @best_pair
     end
 
@@ -680,6 +680,8 @@ module Bio::DB::Primer3
 
     def add_primers_file(filename)
       Primer3Record.parse_file(filename) do | primer3record |
+      #  puts "#{primer3record.snp.to_s}:#{primer3record.chromosome}"
+       # puts @snp_hash.keys.to_s
         current_snp = @snp_hash["#{primer3record.snp.to_s}:#{primer3record.chromosome}"]
         current_snp.add_record(primer3record)
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.4.5
+  version: 0.4.6
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-04 00:00:00.000000000 Z
+date: 2014-10-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio