bio-polyploid-tools 1.0.0 → 1.2.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -7,13 +7,18 @@ addons:
     - libncurses5-dev
     - libtinfo-dev 
     - exonerate  
+    - blast2
+    - ncbi-blast+
+    - mafft
+    - primer3
 before_install:
   - gem update --system
   - export RUBYOPT="-W1"
 rvm:
-  - 2.3.5
-  - 2.4.2
-  - 2.5.0
-  - 2.6.0
+  - 2.3
+  - 2.4
+  - 2.5
+  - 2.6
+  - 2.7
 
 

data/SECURITY.md

@@ -0,0 +1,16 @@
+# Security Policy
+
+## Supported Versions
+
+The following table shows the currently supported version. 
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 1.1.x   | :white_check_mark: |
+| 1.0.x   | :x:                |
+| 0.x.x   | :x:                |
+
+
+## Reporting a Vulnerability
+
+If you find a vulneravility, please submit a comment in the security tab

data/VERSION

@@ -1 +1 @@
-1.0.0
+1.2.1

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[: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!
 
 
@@ -283,18 +288,19 @@ file.close
 #chr_group = chromosome[0]
 write_status "Searching markers in genome"
 exo_f = File.open(exonerate_file, "w")
+contigs_f = nil
 contigs_f = File.open(temp_contigs, "w") if options[:extract_found_contigs]
 filename=path_to_contigs 
 #puts filename
 target=filename
 
-fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
+fasta_file = Bio::DB::Fasta::FastaFile.new(fasta: target)
 fasta_file.load_fai_entries
 
 found_contigs = Set.new
 
 
-def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
+def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options, contigs_f: nil)
   if aln.identity > min_identity
     exo_f.puts aln.line
     unless found_contigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file. 
@@ -312,11 +318,11 @@ def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
 end
 
 Bio::DB::Blast.align({:query=>temp_fasta_query, :target=>options[:database], :model=>model, :max_hits=>options[:max_hits]}) do |aln|
-  do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options)
+  do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options, contigs_f: contigs_f)
 end if options[:aligner] == :blast
 
 Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model}) do |aln|
-  do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
+  do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options, contigs_f: contigs_f)
 end if options[:aligner] == :exonerate
  
 exo_f.close() 
@@ -362,7 +368,7 @@ 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/bin/polymarker_capillary.rb

@@ -53,7 +53,7 @@ OptionParser.new do |opts|
     options[:markers] = o
   end
 
-  opts.on("-o", "--output_folder FOLDER", "Path to a folder where the outputs are going to be stored") do |o|
+  opts.on("-o", "--output FOLDER", "Path to a folder where the outputs are going to be stored") do |o|
     options[:output_folder] = o
   end
   opts.on("-g", "--genomes_count INT", "Number of genomes (default 3, for hexaploid)") do |o|
@@ -146,7 +146,7 @@ module Bio::PolyploidTools
       snp
     end
 
-    def primer_3_all_strings(target_chromosome, parental) 
+    def primer_3_all_strings(target_chromosome, parental, max_specific_primers: 20, flanking_size:500) 
       #puts target_chromosome 
       #puts parental
       #puts aligned_sequences.to_fasta
@@ -155,8 +155,11 @@ module Bio::PolyploidTools
 
       seq_original = String.new(pr.sequence)
       #puts seq_original.size.to_s << "-" << primer_3_min_seq_length.to_s
+      #puts "___"
+      #puts pr.inspect
       return primer_3_propertes if seq_original.size < primer_3_min_seq_length
-      return primer_3_propertes unless pr.snp_pos == 500
+      #puts "((("
+      return primer_3_propertes unless pr.snp_pos == flanking_size
       #puts "Sequence origina: #{ self.original}" 
       #puts pr.to_fasta
       #puts "Postion: #{pr.snp_pos}"
@@ -274,9 +277,9 @@ file.close
 exo_f = File.open(exonerate_file, "w")
 target=reference
 
-fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
+fasta_file = Bio::DB::Fasta::FastaFile.new(fasta: target)
 fasta_file.load_fai_entries
-min_identity = 95
+min_identity = 90
 found_contigs = Set.new
 
 
@@ -361,7 +364,7 @@ class Bio::DB::Primer3::Primer3Record
 end
 
 printed_counts = Hash.new(0)
-Bio::DB::Primer3::Primer3Record.parse_file(primer_3_output) do | primer3record |
+Bio::DB::Primer3::Primer3Record.parse_file(primer_3_output ) do | primer3record |
   #puts primer3record.inspect
   next if primer3record.primer_left_num_returned.to_i == 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 1.2.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "1.0.0"
+  s.version = "1.2.1"
 
   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 = "2019-07-05"
+  s.date = "2021-05-10"
   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]
@@ -23,6 +23,7 @@ Gem::Specification.new do |s|
     "Gemfile",
     "README.md",
     "Rakefile",
+    "SECURITY.md",
     "VERSION",
     "bin/bfr.rb",
     "bin/blast_triads.rb",
@@ -100,6 +101,11 @@ Gem::Specification.new do |s|
     "lib/bio/db/exonerate.rb",
     "lib/bio/db/primer3.rb",
     "lib/bioruby-polyploid-tools.rb",
+    "test/data/7B_amplicon_test.fa",
+    "test/data/7B_amplicon_test.fa.fai",
+    "test/data/7B_amplicon_test_reference.fa",
+    "test/data/7B_amplicon_test_reference.fa.fai",
+    "test/data/7B_marker_test.txt",
     "test/data/BS00068396_51.fa",
     "test/data/BS00068396_51_blast.tab",
     "test/data/BS00068396_51_contigs.aln",
@@ -129,6 +135,13 @@ Gem::Specification.new do |s|
     "test/data/PST130_7067.csv",
     "test/data/PST130_7067.fa",
     "test/data/PST130_7067.fa.fai",
+    "test/data/PST130_7067.fa.ndb",
+    "test/data/PST130_7067.fa.nhr",
+    "test/data/PST130_7067.fa.nin",
+    "test/data/PST130_7067.fa.not",
+    "test/data/PST130_7067.fa.nsq",
+    "test/data/PST130_7067.fa.ntf",
+    "test/data/PST130_7067.fa.nto",
     "test/data/PST130_reverse_primer.csv",
     "test/data/S22380157.fa",
     "test/data/S22380157.fa.fai",
@@ -178,34 +191,27 @@ Gem::Specification.new do |s|
     "test/test_blast.rb",
     "test/test_exon_container.rb",
     "test/test_exonearate.rb",
+    "test/test_integration.rb",
     "test/test_snp_parsing.rb",
     "test/test_wrong_selection.sh"
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.7.7".freeze
+  s.rubygems_version = "3.1.4".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then
     s.specification_version = 4
+  end
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<bio>.freeze, [">= 1.5.1"])
-      s.add_runtime_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
-      s.add_runtime_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
-      s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2"])
-      s.add_development_dependency(%q<shoulda>.freeze, [">= 2.10"])
-      s.add_development_dependency(%q<test-unit>.freeze, [">= 0"])
-      s.add_development_dependency(%q<juwelier>.freeze, [">= 0"])
-    else
-      s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
-      s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
-      s.add_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
-      s.add_dependency(%q<systemu>.freeze, [">= 2.5.2"])
-      s.add_dependency(%q<shoulda>.freeze, [">= 2.10"])
-      s.add_dependency(%q<test-unit>.freeze, [">= 0"])
-      s.add_dependency(%q<juwelier>.freeze, [">= 0"])
-    end
+  if s.respond_to? :add_runtime_dependency then
+    s.add_runtime_dependency(%q<bio>.freeze, [">= 1.5.1"])
+    s.add_runtime_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+    s.add_runtime_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
+    s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2"])
+    s.add_development_dependency(%q<shoulda>.freeze, [">= 2.10"])
+    s.add_development_dependency(%q<test-unit>.freeze, [">= 0"])
+    s.add_development_dependency(%q<juwelier>.freeze, [">= 0"])
   else
     s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
     s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])

data/lib/bio/BFRTools.rb

@@ -31,7 +31,7 @@ module Bio::BFRTools
     BASES = [:A, :C, :G, :T]
     #Sets the reference file
     def reference(path)
-      @reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      @reference_db = Bio::DB::Fasta::FastaFile.new(fasta: path)
       @reference_path = path
     end
 
@@ -49,7 +49,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @parental_1_name = opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @parental_1_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @parental_1_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @parental_1_path = path
 
     end 
@@ -61,7 +61,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @parental_2_name = @name = opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @parental_2_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @parental_2_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @parental_2_path = path
     end
 
@@ -72,7 +72,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @bulk_1_name =  opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @bulk_1_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @bulk_1_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @bulk_1_path = path
     end 
 
@@ -83,7 +83,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @bulk_2_name =  opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @bulk_2_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @bulk_2_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @bulk_2_path = path
     end     
 

data/lib/bio/BIOExtensions.rb

@@ -64,7 +64,7 @@ end
 
 class Bio::NucleicAcid
 
-  IUPAC_CODES = {
+  IUPAC_CODES ||= {
 
     'y' => 'ct',
     'r' => 'ag',

data/lib/bio/PolyploidTools/ExonContainer.rb

@@ -18,7 +18,7 @@ module Bio::PolyploidTools
     end
 
     def gene_models(path)
-      @gene_models_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      @gene_models_db = Bio::DB::Fasta::FastaFile.new(fasta: path)
       @gene_models_db.index
       @gene_models_path = path
     end
@@ -48,7 +48,7 @@ module Bio::PolyploidTools
 
     #Sets the reference file for the gene models
     def chromosomes(path)
-      @chromosomes_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      @chromosomes_db = Bio::DB::Fasta::FastaFile.new(fasta: path)
       @chromosomes_path = path
     end
 
@@ -72,7 +72,7 @@ module Bio::PolyploidTools
       name = opts[:name]
       path = opts[:reference_path]
       path = opts[:alig_path]
-      chromosomes[name] = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      chromosomes[name] = Bio::DB::Fasta::FastaFile.new(fasta: path)
     end
     
     def add_snp(snp)
@@ -109,7 +109,7 @@ module Bio::PolyploidTools
       ret_str = ""
       @parents.each  do |name, bam|
         ret_str << ">#{gene_region.id}_SNP-#{snp.position}_#{name} Overlapping_exons:#{gene_region.to_s} localSNPpo:#{local_pos_in_gene+1}\n" 
-        to_print =  bam.consensus_with_ambiguities({:region=>gene_region}).to_s
+        to_print =  bam.consensus_with_ambiguities(region: gene_region).to_s
         to_print[local_pos_in_gene] = to_print[local_pos_in_gene].upcase
         ret_str << to_print << "\n"
       end
@@ -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/NoSNPSequence.rb

@@ -222,7 +222,7 @@ module Bio::PolyploidTools
         end
     end
 
-    def primer_3_all_strings(target_chromosome, parental) 
+    def primer_3_all_strings(target_chromosome, parental, max_specific_primers: nil) 
       #puts "primer_3_all_strings: #{target_chromosome} #{parental}"
       pr = primer_region(target_chromosome, parental )
       #puts pr.inspect

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
@@ -402,9 +402,16 @@ module Bio::PolyploidTools
       else
         @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
+      #puts "skip_specific: #{skip_specific}: #{total_candidates} > #{max_specific_primers}"
       pr.chromosome_specific.each do |pos|
-
+        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}"
@@ -412,41 +419,38 @@ module Bio::PolyploidTools
         primer_3_propertes << return_primer_3_string(args)
       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 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_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)
-
       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 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_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)
       end
 
       pr.almost_crhomosome_specific_intron.each do |pos|
+        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)
-
       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 +462,8 @@ 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
 

data/lib/bio/db/primer3.rb

@@ -30,18 +30,21 @@ 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={})
     puts "Primer3.run running..."
-
+    timeout = 600
     f_in=opts[:in]
     f_out=opts[:out]
+    timeout = opts[:timeout] if opts[:timeout]
     opts.delete(:in)
     opts.delete(:out)
     primer_3_in = File.read(f_in)
-    status = systemu "primer3_core", 0=>primer_3_in, 1=>stdout='', 2=>stderr=''
+    status = systemu "primer3_core", 0=>primer_3_in, 1=>stdout='', 2=>stderr='' do |cid|
+      sleep timeout
+      Process.kill 9, cid
+    end
     # $stderr.puts cmdline
     if status.exitstatus == 0
       File.open(f_out, 'w') { |f| f.write(stdout) }

data/test/data/7B_amplicon_test.fa

@@ -0,0 +1,12 @@
+>chr7B:1000-1600
+TTTCAAATGCTTGTAAGATATCTGACATCAAGGGGCGATCCCGAAAGTCATACTCGAAGC
+AGCTAGGAAGGACATTCTCAACCTCTGCAGGTAAGTTGTACGGGAATATCGGTTTCTCTT
+TCTTCAGGACAACCAACTGATAAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGC
+CAGTGAACATCTCAAGAATGCTGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTG
+GACCTCTGATGTTTGGTTGCCACTGCTCTGGGGCCATGTAATTTGGAGTTCCAAGTCTTT
+GGATAAGCTCTGGGTTTGGCAGCGACAGTCCAAACAGCAAGGATGGAATCCCAAAATCCC
+CCAGCACAGCATGGTCATGGTCATCAAGGAGAAAATTGCAAGGTTTGAGATTAAGAACAA
+ATATTCCCCTGGAGTGTAGGTCTAGCACACCACGCGCCAAATCGGCGCCGTATCTGCAAA
+TTACAGGAAATAATAAAAATATGTACCACTCAAGAAAACATCCTCTAAACAGAGCATCAT
+AAGCATTCTCAAAAGTCAACCAGGATAATGTGCCTGCACTAAGGTGATGAAGGATATCTG
+C

data/test/data/7B_amplicon_test.fa.fai

@@ -0,0 +1 @@
+chr7B:1000-1600	601	17	60	61

data/test/data/7B_amplicon_test_reference.fa

@@ -0,0 +1,110 @@
+>chr7A
+CTTCCTGCTGCTGAACTTTCTGAGGATCACCGCCCTGATCGGAGACGCTGGCGACCTTTC
+GACTCCTTGGCCTTGTGATGCTCTTGCCGACAAAGATACCTAGCTTCATAGCAGTAAAGA
+AACCTATGGCGATGAACAGAGGCCTCACCACCCAATGGAAGTCCTCGAGGTGCTCATACT
+TCTTCACAACCCCATCGCACTTGTCGAAGCTCACCACCTCCACCTCTGAAGGGTCGGCCA
+AGCAGCTGCACACTTCGCCAAGGCTGAATTTGCCAGGGAAGGTCACAACAAGGCATCCAT
+TCGAGAGTATCTGTGAAATACGGCCTGTGGCAAACACTCCGCCTCTCTTTCGCGGCCATT
+CAAACCGGGGGCTTGATGTGTTAGTTCTCAGCCTCACAAATTGTCCCACGCAGTAGGCTT
+CGGCCATTTGCAGATCTGAATATTCCCCCTTCCAGAGGGTGTCCATTCCTATTAAACCAA
+CATACACGGTGCCATTACGGTCAATGCTATGAAGAATTCCGACCTGAGACCGCTTCTTGT
+CTTCCTCCCTAAGCCTTACCCAGTCTCCGGCAGCGAAACCATAGGTCACCCTCTCCACTG
+TCGAGGAATGGACCTTCAAAGGGTCATGTATTCCATGGACTCGTACAAGAATGTAGCTAT
+CACGTTCTCCATCCTCCTCCATGCCAACTATGGTTCCATCAGGAATTTCCATTGTTTCAG
+GAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCACCAACTTGCAGCTTATCCT
+TAAAGTGTGACCAATTAGTGTGACTTGGCACTACTGCCCTTGGGTTTTCAGAACTATCCC
+AGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAATGAAAAAAGAAAACAAATT
+TAGGAAAGAACTATGGTAAAATCACCCATCTGATGGCAGTTTAACCAAATACTGCAAGTT
+GATAAGGCAGAAGTAGAAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGCAAGATAT
+CTGACATCAAGGGGCGATCCCGAAAGTCGTACTCAAAGCAGCTAGAAAGGACATTCTCAA
+CCTCTGCAGGTAAGTTGTATGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
+AAATTTCATCTGGTGATTTGCCACGCCAAGGCTGAACGCCACTGAACATCTCAAGAATGC
+TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
+ATTGCTCTGGGGCCATGTAATTTGGAGTCCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
+GAGAAAGTCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAGCACAGCATGGTCATGGT
+CATCAAGGAGAAAATTGCAAGGCTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
+CTAGCACACCACGCGCCAAATCGGCACCATATCTGCAAGTTATAAGAATTCATAAAAATA
+TGTATTACTACTCAAGAAAATATCTTCTAAACAGAGCATCATAAGCATTCTCAAAAGTCA
+ACAGGATAATGTGCCTGTACTAAGGTCATAAACTATATCTGCCAGTTAATCAATCAACAC
+GTTCACTGGTAGAAAGTTGGAAACTGCATGCTTAGGTGACACTTCATCTAAAAAAAATGT
+ATATTTGTCTCTGATAAATTGTATTCTTAAGATAAGCCGACGAACACTCAGAGTATTCAG
+AACATCAAATATGTTCAAAACTGTGGAGACTTCCACAATACCTTAAAACATCCGACAAAG
+GGAGCCTTCCACCTTTAAGCCGAGCCATCTTGTCCCCGATGGATCCTTCATAAAACTTCA
+TCGCTATGCAAAGCTGAAAATCCATGAAACAAAAATTAAGCCACAACGCCATCTTTCATT
+CACAGGTGACCCAACAGCAAGGCTTTGCCAGACAAAAACATACCCTCCCATTCTGCGTTG
+AGATGCCATGTAGGAAGCAGACATTGCCCAGGCCCTGGCATTTGCCGAACACCTCGTCGA
+ACCTCGCCGAGAACACCTGCAGCTGGTCGTCCCTGACCGGGTGCATCATCTTCACGGCG
+>chr7B
+GTGCACTTCTTGCTGCTGAACTTTCTGAGGATCGGCACCCTGATCGGAGACGCTGGCGAC
+CTTTCGACTCCTTGGCCTTGTGATGCTCTTCCCGACGAACACACCTAGCTTCATAGCAGT
+AAAGAAACCTATGGCGATGAACAGAGGTCTTACCGCCCAATGGAAGTCCTCGAGGTGCTC
+ATACTTCTTCACAACCCCCTCGCACTTGTCGAAGCTCACCACCTCCACCTCAGAAGGGTC
+GGCCAAGCAGCTGCACACTTCGCCAAGGCTCAACTTGCCAGGGAAGGTCACAACAAGGCA
+TCCATTCGAGAGTATCTGTGAAATACGGCCTGTGGCAAACACCCCGCCTCTCTTTCGCTG
+CCATTCGAACCGCGGGCTTGAAGTGTTGGTTCTCAGCCTCACAAATTGTCCCACACAGTA
+GGCTTCGGCCATTTGCAGATCTGAATATTCCCCCTTCCAGAGGGTGTCCATTCCTATCAA
+ACCAACATACACGGTGCCATTGCGGTCGATGCTATGAAGAATTCCGACCTCAGACCGCTT
+CTTGTCTTCCTCCCTGAGCCTTACCCAGTATCCGGCAGCGAAACCATAGGTCACCCTCTC
+CACTGTCGAGGAACGGACCTTCAAAGGGTCATGTATTGCATGGACTCGTACAAGAATGTT
+GCTATCACGTTCTCCATCCTCCATGCCAACTATGGTCCCATCAGGGATTTCCATTGTTTC
+AGGAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCCCCAACTTGCAGCTTATC
+CTTGAAGTGTGACCAGTTAGTGTGACTTGGTGCTACTGCCCTTGGGTTTTCAGAACTGTC
+CCAGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAAGGAAAAAAAAACAAATT
+TAGGGAAGTAACATGGTAAAATCACCCATCCAATGGCAGTTTAACCAAATAGTGCAAGTT
+GATAAGGCAGAAGTAGAAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGTAAGATAT
+CTGACATCAAGGGGCGATCCCGAAAGTCATACTCGAAGCAGCTAGGAAGGACATTCTCAA
+CCTCTGCAGGTAAGTTGTACGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
+AAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGCCAGTGAACATCTCAAGAATGC
+TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
+ACTGCTCTGGGGCCATGTAATTTGGAGTTCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
+GCGACAGTCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAGCACAGCATGGTCATGGT
+CATCAAGGAGAAAATTGCAAGGTTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
+CTAGCACACCACGCGCCAAATCGGCGCCGTATCTGCAAATTACAGGAAATAATAAAAATA
+TGTACCACTCAAGAAAACATCCTCTAAACAGAGCATCATAAGCATTCTCAAAAGTCAACC
+AGGATAATGTGCCTGCACTAAGGTGATGAAGGATATCTGCCAGTTAATCAACCAACACGT
+TCACTGGTAGAAAGTTGGAAACTGCATGCTTAGGTGACAATTCATCTAAAAAAACTGTAT
+ATTTGCCTCTGGTAAACTGTATTCTTAAGATAAGCCGACAAACATTCAGTATTCAGAACA
+TCAATATGTACAGAACTGTGGAGACTTCCACCATACCTTAAAACATCTGACAAAGGGAGC
+CTTCCACCTTTAAGCCGAGCCATCTTGTCCCCGACGGATCCTTCGTAAAACTTCATCGCT
+ATGCAAAGCTGAAAATCCATGAAACAAAAATTAAGCCACAGCACCATCTTTCATTCACAG
+GTGACCCAACAGCAAGGCTATGCCAGACAGAGAACATACCCTCCCATTCTGCGTCGAGAT
+GCCATGTAGGAAGCAGACATTGCCCAGGCCCTGGCACTTGCCGAACACCTCGTCGAACCT
+CGCCGAGAACACCTGCAGCTGGTCGTCCCTGACCGGGTGCAGCATCTTCACAGCGACCTC
+G
+>chr7D
+GTTGTGCACTTCTTGCTGCTGAACTTTCTGAGGATCGGCACCCTGATCAGAGACGCTGGC
+GACCTTTCGACTCCTTGGCCTTGTGATGCTCTTCCCAACAAAGACACCTAGCTTCATAGC
+AGTAAAGAAACCTATGGCAATGAACAGAGGCCTCACCGCCCAATGGAAGTCCTCGAGGTG
+CTCATACTTCTTCACAACGCCCTCGCACTTGTCGAAGCTCACCACCTCCACCTCTGAAGG
+GTCGGCCAAGCAGCTGCACACTTCGCCAAGGCTGAATTTGCCAGGGAAGGTCACAGCAAG
+GCATCCATTCGAGAGTATCTGTGAAATACGGCCTATGGCGAACACTCCGCCTCTCTTTCG
+CGGCCATTCAAACCGGGGGCTTGAAGTGTTAGTTCTGAGCCTCACAAATTGTCCCATGCA
+GTAGGCTTCGGCCATTTGCAGATCTGAATATTCCCCCTTCCACAGGGTGTCCATTCCTAT
+CAAACCAACATACACGGTGCCATTACGGTCAATGCTATGAAGAATTCCGACCTGAGACCG
+CTTCTTGTCTTCCTCCCTAAGCCTTACCCAGTCTCCGGCAGCGAAACCATAGGTCACCCT
+CTCCACTGCTGAGGAACGGACCTTCAGAGGGTCATGTATTCCATGGACTCGTACAAGAAT
+GTAGCTATCGCGTTCTCCATCCTCCATGCCAACTATGGTTCCATCAGGGATTTCCATTGT
+TTCAGGAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCACCAACTTGCAGCTT
+ATCCTTGAAGTGTGACCAATTAGTGTGACTTGGCACTACTGCCCTTGGGTTTTCAGAACT
+ATCCCAGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAATGAAAAAAGAAAAC
+AAATTTAGGGAAGAACCATAGTAAATCACCCATCCAATGGCAGTTTAACCAAATACTGCA
+AGTTGATAAGGTAGAAGAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGTAAGATAT
+CTGACATCAAGGGGCGATCCCGAAAGTCGTACTCAAAGCAGCTAGAAAGGACATTCTCAA
+CCTCTGCAGGTAAATTGTACGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
+AAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGCCACTGAACATCTCAAGAATGC
+TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
+ATTGCTCTGGGGCCATGTAATTTGGAGTCCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
+GCGACAGCCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAACACAGCATGGTCATGAT
+CATCAAGGAGAAAATTACAAGGCTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
+CCAGCACACCACGTGCCAAATCAGCGCCATATCTGCAAGTTATAAGAATTCATAAAAATA
+TGTACTACTCCAAACAGAGCATCATAAGCATTCTCAAAAGTCAACAGGATCATTTGCCTG
+CACTAAGGTGATAAACTAGATCTGCCAGTTAATCAATCAACACGTTCACTGGTAGAAAGT
+TGGAAACTGCATGCTTAGGTGACACTTCATCTAAAAAACTGTATATTTGCCTCTGTGGTA
+AACTGTATTCTTAAGATAAGCCGACGAACATTCAGTATTCAGGACATCAAATATGTTCAA
+AACTGTGGAGACTTCCACCATACCTTAAAACATCTGACAAAGGGAGCCTTCCACCTTTAA
+GCCGAGCCATCTTGTCCCCGACGGATCCTTCATAGAACTTCATCACTATGCAAAGCTGAA
+AATCCATGAAACAAAAATTAAGCCACAACGCCATCTTTCATTCACAGGCGACCCAACAGC
+AAGGCTATGCCAGACAAAAACATACCCTCCCATTCTGCGTCGAGATGCCATGTAGGAAGC
+AGACATTGCCCAGGCCCTGGCATTTGCCAAACACCTCGTCGAACCTCGCCGAGAACACCT
+GCAGCTGGTCGTCCCTGACCGGGTGCAGCATCTTCACGGCGACCTCGTGGTACCGGTCAT
+A

data/test/data/7B_amplicon_test_reference.fa.fai

@@ -0,0 +1,3 @@
+chr7A	2099	7	60	61
+chr7B	2101	2148	60	61
+chr7D	2101	4292	60	61

data/test/data/7B_marker_test.txt

@@ -0,0 +1 @@
+RAC875_c8221_649,7B,CGTACAATTTACCTGCAGAGGTTGAGAATGTCCTTTCTAGCTGCTTTGAG[T/C]ACGACTTTCGGGATCGCCCCTTGATGTCAGATATCTTACAAGCATTTGAA

data/test/test_bfr.rb

@@ -26,12 +26,12 @@ class TestPolyploidTools < Test::Unit::TestCase
     @f2_b=data_path + "/LIB1719.bam"
     
     @bfr_path=data_path + "/bfr_out_test.csv"
-    @fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>@ref})
+    @fasta_db = Bio::DB::Fasta::FastaFile.new(fasta: @ref)
     @fasta_db.load_fai_entries
-    @bam_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@a})
-    @bam_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@b})
-    @bam_f2_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_a})
-    @bam_f2_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_b})
+    @bam_a =  Bio::DB::Sam.new(fasta: @ref, bam: @a)
+    @bam_b =  Bio::DB::Sam.new(fasta: @ref, bam: @b)
+    @bam_f2_a =  Bio::DB::Sam.new(fasta: @ref, bam: @f2_a)
+    @bam_f2_b =  Bio::DB::Sam.new(fasta: @ref, bam: @f2_b)
    # puts "SETUP"
   end
   
@@ -49,8 +49,8 @@ class TestPolyploidTools < Test::Unit::TestCase
     
     #puts @bam_a.methods
     ref_seq=@fasta_db.fetch_sequence(region)
-    reg_a = @bam_a.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
-    reg_b = @bam_b.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
+    reg_a = @bam_a.fetch_region(region: region,  min_cov: min_cov, A: 1)
+    reg_b = @bam_b.fetch_region(region: region,  min_cov: min_cov, A: 1)
     cons_1 = reg_a.consensus
     cons_2 = reg_b.consensus
     
@@ -85,10 +85,10 @@ class TestPolyploidTools < Test::Unit::TestCase
     container = Bio::BFRTools::BFRContainer.new
     
     container.reference @ref
-    container.parental_1  ( {:path => @a } )
-    container.parental_2  ( {:path => @b } )
-    container.bulk_1 ( {:path => @f2_a  })
-    container.bulk_2 ( {:path => @f2_b  })
+    container.parental_1( path:  @a )
+    container.parental_2( path:  @b )
+    container.bulk_1( path:  @f2_a  )
+    container.bulk_2( path:  @f2_b  )
 
     i = -1
 

data/test/test_integration.rb

@@ -0,0 +1,76 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+
+tmp_verb = $VERBOSE
+$VERBOSE=nil
+#puts path
+require path
+require 'bio-samtools'
+require "test/unit"
+$VERBOSE=tmp_verb
+
+
+class TestInregration < Test::Unit::TestCase
+
+  
+  #Set up the paths
+  def setup
+    @data_path= File.expand_path(File.dirname(__FILE__)   + '/data/' )
+    
+    @ref="#{@data_path}/7B_amplicon_test_reference.fa"
+    @amplicon = "#{@data_path}/7B_amplicon_test.fa"
+    @genomes_count = 3
+    @output_folder="#{@data_path}/test_out"
+    @bin=File.expand_path(File.dirname(__FILE__) + '/../bin')
+    @marker = "#{@data_path}/7B_marker_test.txt"
+    FileUtils.rm_r(@output_folder, force: true) if Dir.exist? @output_folder
+
+    cmd = "makeblastdb -in #{@ref} -dbtype nucl "
+    #status, stdout, stderr = 
+    systemu cmd
+    # @ref=data_path + '/S22380157.fa'
+    # @a=data_path + "/LIB1721.bam"
+    # @b=data_path + "/LIB1722.bam"
+    # @f2_a=data_path + "/LIB1716.bam"
+    # @f2_b=data_path + "/LIB1719.bam"
+    
+    # @bfr_path=data_path + "/bfr_out_test.csv"
+    # @fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>@ref})
+    # @fasta_db.load_fai_entries
+    # @bam_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@a})
+    # @bam_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@b})
+    # @bam_f2_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_a})
+    # @bam_f2_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_b})
+   # puts "SETUP"
+
+  end
+  
+  def teardown
+    FileUtils.rm_r(@output_folder, force: true) if Dir.exist? @output_folder
+    Dir.glob("#{@ref}.n*").each do |file| 
+      #puts file 
+      File.delete(file)
+    end
+  end
+  
+  def test_amplicon_primers
+    cmd = "ruby #{@bin}/polymarker_capillary.rb --reference #{@ref} --sequences #{@amplicon}  --genomes_count #{@genomes_count}  --output #{@output_folder} --database #{@ref}"
+    status, stdout, stderr = systemu cmd
+    assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+   
+  end
+
+  def test_deletion_primers
+    cmd = "ruby #{@bin}/polymarker_deletions.rb --reference #{@ref} --sequences #{@amplicon}  --genomes_count #{@genomes_count}  --output #{@output_folder} --database #{@ref}"
+    status, stdout, stderr = systemu cmd
+     assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+  end
+
+  def test_polymerker
+    cmd = "ruby ./bin/polymarker.rb -m #{@marker} -c #{@ref} --extract_found_contigs  -A blast -a nrgene --output #{@output_folder}"
+    status, stdout, stderr = systemu cmd
+     assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+  end
+
+end

data/test/test_snp_parsing.rb

@@ -27,7 +27,7 @@ class TestSNPparsing < Test::Unit::TestCase
   def test_mutant_snp
 
     ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
-    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
     fasta_reference_db.index
     fasta_reference_db.load_fai_entries 
     
@@ -49,7 +49,7 @@ class TestSNPparsing < Test::Unit::TestCase
 
   def test_vcf_line
     ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
-    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
     
     fasta_reference_db.load_fai_entries 
     vcf="IWGSC_CSS_1AL_scaff_1455974	127	test_snp	C	T	135.03	.	"
@@ -85,7 +85,7 @@ class TestSNPparsing < Test::Unit::TestCase
   def test_reference_snp
 
     ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
-    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
     
     fasta_reference_db.load_fai_entries 
     

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.2.1
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2019-07-05 00:00:00.000000000 Z
+date: 2021-05-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -145,6 +145,7 @@ files:
 - Gemfile
 - README.md
 - Rakefile
+- SECURITY.md
 - VERSION
 - bin/bfr.rb
 - bin/blast_triads.rb
@@ -222,6 +223,11 @@ files:
 - lib/bio/db/exonerate.rb
 - lib/bio/db/primer3.rb
 - lib/bioruby-polyploid-tools.rb
+- test/data/7B_amplicon_test.fa
+- test/data/7B_amplicon_test.fa.fai
+- test/data/7B_amplicon_test_reference.fa
+- test/data/7B_amplicon_test_reference.fa.fai
+- test/data/7B_marker_test.txt
 - test/data/BS00068396_51.fa
 - test/data/BS00068396_51_blast.tab
 - test/data/BS00068396_51_contigs.aln
@@ -251,6 +257,13 @@ files:
 - test/data/PST130_7067.csv
 - test/data/PST130_7067.fa
 - test/data/PST130_7067.fa.fai
+- test/data/PST130_7067.fa.ndb
+- test/data/PST130_7067.fa.nhr
+- test/data/PST130_7067.fa.nin
+- test/data/PST130_7067.fa.not
+- test/data/PST130_7067.fa.nsq
+- test/data/PST130_7067.fa.ntf
+- test/data/PST130_7067.fa.nto
 - test/data/PST130_reverse_primer.csv
 - test/data/S22380157.fa
 - test/data/S22380157.fa.fai
@@ -300,13 +313,14 @@ files:
 - test/test_blast.rb
 - test/test_exon_container.rb
 - test/test_exonearate.rb
+- test/test_integration.rb
 - test/test_snp_parsing.rb
 - test/test_wrong_selection.sh
 homepage: http://github.com/tgac/bioruby-polyploid-tools
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -321,9 +335,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
-signing_key: 
+rubygems_version: 3.1.4
+signing_key:
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology
 test_files: []