bio-polyploid-tools 0.3.3 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 381e678b7d15cffb675e941b461ccd7a8cbc1132
-  data.tar.gz: bb2632d78ed15718ea6e295de21539e158896625
+  metadata.gz: 612c7e5e39e8908003387efe2e6ba739b7fb981d
+  data.tar.gz: eac406e26c6985115884ba53f0c3dadf22bf3e81
 SHA512:
-  metadata.gz: 7c3c364a4fc0bdd6e20aa69eacb9e76c90e1a8b34de50775ce5a77177d4438c3f0b768e73e751f282bfa14dc88645e8e19c1c69c0ce4d60d9c01d5371bb0ea08
-  data.tar.gz: f16d826561a31ac8d045ca9934068f6f7f2101d306405c5c5d0d0aaa8bc8976039fcc3d0f5f3d0170f08f150257e914a135a706f1f07ae8b6e85b0572d46cb0c
+  metadata.gz: c9408f36825e70458901b867b3733d878291240b937d120be658c71e5b7d53f22ae2c7023408a9cfb2be385a630ed1fae4e0e321160d6556820baa36a657bc7a
+  data.tar.gz: 84bf294ab30e62fe758b54274adcca0c1f0f5331a0bc56a2932b2af9d112518c45535b59496f7f33365ef70d10a578946d398b095da473fd5d0af857383f1c10

data/VERSION

@@ -1 +1 @@
-0.3.3
+0.4.0

data/bin/polymarker.rb

@@ -35,6 +35,19 @@ options[:bucket_size] = 0
 options[:bucket] = 1
 options[:model] = "est2genome"
 options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
+options[:flanking_size] = 100;
+options[:primer_3_preferences] = {
+      :primer_product_size_range => "50-150" ,
+      :primer_max_size => 25 , 
+      :primer_lib_ambiguity_codes_consensus => 1,
+      :primer_liberal_base => 1, 
+      :primer_num_return=>5,
+      :primer_thermodynamic_parameters_path=>File.expand_path(File.dirname(__FILE__) + '../../conf/primer3_config/') + '/'
+
+    }
+
+
+
 OptionParser.new do |opts|
   opts.banner = "Usage: polymarker.rb [options]"
 
@@ -66,9 +79,21 @@ OptionParser.new do |opts|
     options[:arm_selection] = arm_selection_functions[o.to_sym];
    end
   
+  opts.on("-p", "--primer_3_preferences FILE", "file with preferences to be sent to primer3") do |o|
+    options[:primer_3_preferences] = Bio::DB::Primer3.read_primer_preferences(o, options[:primer_3_preferences] )
+  end
     
 end.parse!
 
+if options[:primer_3_preferences][:primer_product_size_range]
+  range = options[:primer_3_preferences][:primer_product_size_range]
+  range_arr = range.split("-")
+  min = range_arr[0].to_i
+  max = range_arr[1].to_i
+  raise  Bio::DB::Exonerate::ExonerateException.new "Ragne #{range} is invalid!" unless max > min
+  options[:flanking_size] = max
+end
+
 p options
 p ARGV
 
@@ -111,6 +136,8 @@ end
 min_identity= 90
 snps = Array.new
 
+begin
+  
 write_status "Loading Reference"
 #0. Load the fasta index 
 fasta_reference_db = nil
@@ -124,7 +151,6 @@ end
 
 
 #1. Read all the SNP files 
-#All the SNPs should be on the same chromosome as the first SNP. 
 #chromosome = nil
 write_status "Reading SNPs"
 File.open(test_file) do | f |
@@ -140,7 +166,7 @@ File.open(test_file) do | f |
        region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
        snp.template_sequence = fasta_reference_db.fetch_sequence(region)
      else
-        $stderr.puts "Unable to find entry for #{snp.gene}"
+        $stderr.puts "ERROR: Unable to find entry for #{snp.gene}"
       end
 
     else
@@ -149,7 +175,12 @@ File.open(test_file) do | f |
     rise Bio::DB::Exonerate::ExonerateException.new "No SNP for line '#{line}'" if snp == nil
     snp.snp_in = snp_in
     snp.original_name = original_name
-    snps << snp
+    if snp.position 
+      snps << snp
+    else
+      $stderr.puts "ERROR: #{snp.gene} doesn't contain a SNP"
+    end
+
 #    chromosome = snp.chromosome unless chromosome
   #  raise Bio::DB::Exonerate::ExonerateException.new "All the snps should come from the same chromosome" if chromosome != snp.chromosome
   end
@@ -207,7 +238,7 @@ write_status "Reading best alignment on each chromosome"
 
 
 container= Bio::PolyploidTools::ExonContainer.new
-container.flanking_size=100
+container.flanking_size=options[:flanking_size] 
 container.gene_models(temp_fasta_query)
 container.chromosomes(temp_contigs)
 container.add_parental({:name=>snp_in})
@@ -227,12 +258,14 @@ container.print_fasta_snp_exones(file)
 file.close
 
 file = File.open(primer_3_input, "w")
-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}/")
+#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}/")
+
+Bio::DB::Primer3.prepare_input_file(file, options[:primer_3_preferences])
 container.print_primer_3_exons(file, nil, snp_in)
 file.close
 
@@ -253,4 +286,11 @@ kasp_container.add_primers_file(primer_3_output)
 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}") }
 
-write_status "DONE"
+write_status "DONE"
+rescue StandardError => e
+  write_status "ERROR\t#{e.message}"
+  raise e 
+rescue Exception => e
+  write_status "ERROR\t#{e.message}"
+  raise e  
+end

data/bin/snp_position_to_polymarker.rb

@@ -0,0 +1,68 @@
+#!/usr/bin/env ruby
+
+#This This script converts the a file with snps and positions with the header:
+#GENE,BASE,POS,SNP,Chromosome
+#  snp.gene, snp.original, snp.position, snp.snp, snp.chromosome 
+#To the input expected by polymarker
+#ID, Chromosome, sequence
+#With sequence containing the SNP in the notation "[A/T]"
+require 'bio'
+require 'optparse'
+
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+require path
+
+
+def log(msg)
+  time=Time.now.strftime("%Y-%m-%d %H:%M:%S.%L")
+  puts "#{time}: #{msg}"
+end
+
+markers = nil
+
+options = {}
+options[:flanking_size] = 100
+OptionParser.new do |opts|
+  
+  opts.banner = "Usage: snp_postion_to_polymarker.rb [options]"
+
+  opts.on("-s", "--sno_file CSV", "CSV file with the following columnns:\nID,Allele_1,position,Allele_1,target_chromosome") do |o|
+    options[:snp_file] = o
+  end
+  opts.on("-r", "--reference FASTA", "reference with the genes/contings/marker seuqnece") do |o|
+    options[:reference] = o
+  end
+  opts.on("-o", "--out CSV", "Output file ") do |o|
+    options[:output] = o
+  end
+  opts.on()("-f", "--flanking_size INT", "Flanking size around the SNP")
+  
+end.parse!
+#reference="/Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa"
+
+fasta_reference = options[:reference] if options[:reference]
+fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>fasta_reference})
+fasta_reference_db.load_fai_entries
+
+out = $stdout
+out = File.open(options[:output], "w") if options[:output]
+File.open(options[:snp_file]) do | f |
+  f.each_line do | line |
+    	snp = nil
+    	snp = Bio::PolyploidTools::SNP.parse(line)
+    	entry = fasta_reference_db.index.region_for_entry(snp.gene)
+    	if entry
+       		region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
+       		snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+
+       		out.puts "#{snp.gene}_#{snp.snp_id_in_seq},#{snp.chromosome},#{snp.to_polymarker_sequence(options[:flanking_size])}"
+    	else
+    	   $stderr.puts "ERROR: Unable to find entry for #{snp.gene}"
+    	end
+	end
+end
+
+out.close if options[:output]
+

data/bio-polyploid-tools.gemspec

@@ -2,19 +2,19 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.3.3 ruby lib
+# stub: bio-polyploid-tools 0.4.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.3.3"
+  s.version = "0.4.0"
 
   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 = "2014-05-30"
+  s.date = "2014-09-25"
   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", "snps_between_bams.rb"]
+  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"]
   s.extra_rdoc_files = [
     "README",
     "README.md"
@@ -36,6 +36,7 @@ Gem::Specification.new do |s|
     "bin/map_markers_to_contigs.rb",
     "bin/markers_in_region.rb",
     "bin/polymarker.rb",
+    "bin/snp_position_to_polymarker.rb",
     "bin/snps_between_bams.rb",
     "bio-polyploid-tools.gemspec",
     "conf/defaults.rb",
@@ -98,19 +99,25 @@ Gem::Specification.new do |s|
     "test/data/LIB1721.bam.bai",
     "test/data/LIB1722.bam",
     "test/data/LIB1722.bam.bai",
+    "test/data/PST130_7067.csv",
+    "test/data/PST130_7067.fa",
+    "test/data/PST130_7067.fa.fai",
+    "test/data/PST130_reverse_primer.csv",
     "test/data/S22380157.fa",
     "test/data/S22380157.fa.fai",
     "test/data/Test3Aspecific.csv",
     "test/data/Test3Aspecific_contigs.fa",
     "test/data/bfr_out_test.csv",
     "test/data/patological_cases5D.csv",
+    "test/data/primer_3_input_header_test",
     "test/data/short_primer_design_test.csv",
     "test/data/test_primer3_error.csv",
     "test/data/test_primer3_error_contigs.fa",
     "test/test_bfr.rb",
     "test/test_exon_container.rb",
     "test/test_exonearate.rb",
-    "test/test_snp_parsing.rb"
+    "test/test_snp_parsing.rb",
+    "test/test_wrong_selection.sh"
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools"
   s.licenses = ["MIT"]

data/lib/bio/PolyploidTools/SNP.rb

@@ -37,7 +37,16 @@ module Bio::PolyploidTools
     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. 
     end
+
+    def to_polymarker_sequence
+      out = template_sequence.clone
+      out[position-1]  = "[#{original}/#{snp}]"
+      out
+    end
     
+    def snp_id_in_seq
+      "#{original}#{position}#{snp}"
+    end
     
     #We Only want the chromosome, we drop the arm. 
     #We don't use this any more. 

data/lib/bio/db/primer3.rb

@@ -3,11 +3,49 @@ module Bio::DB::Primer3
   class Primer3Exception < RuntimeError 
   end
 
+  def self.read_primer_preferences(file, defaults)
+
+    File.open(file) do |f|
+      f.each_line do | line | 
+        line.chomp!
+        arr = line.split("=")
+        defaults[arr[0].downcase.to_sym] = arr[1];
+      end
+    end
+
+    return defaults
+  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 , 
+      :primer_lib_ambiguity_codes_consensus => 1,
+      :primer_liberal_base => 1, 
+      :primer_num_return=>5,
+      :primer_thermodynamic_parameters_path=>File.expand_path(File.dirname(__FILE__) + '../../../../conf/primer3_config/') + '/'
+
+    }.merge(opts2)
+    
+    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..."
 
     f_in=opts[:in]
     f_out=opts[:out]
+    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=''
     # $stderr.puts cmdline

data/test/data/PST130_7067.csv

@@ -0,0 +1 @@
+PST130_7067,T,3334,G,7067

data/test/data/PST130_7067.fa

@@ -0,0 +1,2 @@
+>PST130_7067
+ggggggaggctaacttttggaaatcttttcctttctcttcttttcctatcatcttattatgaacattattattctatctgtgcacggagtgaactattatttattatttttgattgggatattctttttgttttgttttggagtgttattcagtaaggcagtaaggaagagatcagtccttattagttaaagaattctcttctcctttgggtcagaccttttagcgtgcaccacaaagtagcttacggagaagaggccatatttaccctccagctttcatctcaacctacctgtcccggaaacggacaggcaggtagttgctgagtaagttaaataactacttattctacaccaactcacttttctttccatagcgcaaagggccagcctccaaaggatccaaaggagggacttgttggggatactcaaatcttgcactgagagcatccactggtttggtgggcgattttttcccctgccttcacaacacctttgtggagctcaaaaatcacgcctgtgggacctgtttatgcacttttccgtccagcatggttacaaaacaacaacagaatgcttatgctccttagatctccagaggtagaaccaagaacacaagtgttgttgtgatgaagtcaatgagtgaggattcaattccaggcttgttttagataaagcttttcaccttacctagcatgtcttgttaaatagatatactgccgcagcagaatcgtgatgattatccagcaagccttatagtgtcttgcagttttttttgaggtgaagaggacggtagaagatagctacagttgtatgttgtaacgtcagtggactcctcggtagtctcgtttacggagaatggcccagcgaagtctgagccacaaaatatttcgaaaaacttcagtgctcgaagtcacgatagtcatattgcatcagatcaggaacctcaaagaaaattttcgggtgtggtacccaaaatgagcagacccttatttgaaagccaaccatcccgaccgtctaagtttactacttgaggcaagactaggtgtcaagcctctctcagaggctgatttcggaaggagttgaaacgtacaactgcgctcagctcgctgatagatcaagccaagacgaacgagccatcatcatcttagactgcaggaccaacaagccaggaaggtaaatctgtttcatgcattgcgagcacacaatcacgaatcacgggatgttcatttacagttctaaataacaaatggtgaaagtgacaaaaatggcgcgaagaggtttgctagcagttaggacaagccttcaagatcacgacgtatcgtccttcgccgatcggatagacgatataatgcagcaaagatgtttggaagagagcttgtgccagttcgttcaacccatcgagttcacccggtgctctacggatggtttcagagaattgatcatttggttagggtcccgtgtgcttaatagaagttgaaactggaagatagatcagtgatggcgtactgttagtggttccatcgttgtgaaattcggatagactgctgggctaggatactggaacgcaaccaaccgtctttgcttctgatactttgtgaccgcggttgacctttagtcgcagaacatttattggggtgaattcacaagtcttgcgtaatcagacaggcaatttgtgaaagaaatctgactcactgtcagtttgtaccgaggacaacaccagagcacgtcatgcggagcacatgttgggggatccaccgcgatgtctttcattccacatcaacagaggaaaaaacatgagcgtggtcaactctaagcgtgatttgaggagggaaaaaaagaatcacaaagattcctgtcgctttccttgccattgctgcacgcaggccacggagtgtcgccgctgcacttcgacgatacgaactcgctaagaccaaagacgcaaagtagaagtgcgggtttcatgaagttcatggtatcgaacaggcgacggggagtgcgatagggctgaagatgaagtggatgcttgtggatttgagggtgagttcgagaaaaatatgtgagttgttgacttctgagggcggccgaagtgaaaccactcgcctgttatatacatttccgaaagaagcctttcaaatgtatcaggtgtaatccaatcaccgaagattcctgcaaaaccttcagctgaggaatagacagcgggatgatttccccgacgacggtacagtcacagtgcccggtggcaccgcaggataacacacaaccccgtcgaaagctgtagctaacggggccgtcaagttgggccctgtgtggcctcggcgtactggctggcgaccctgagggtctccttggctttatacgattgcgtcgtgagcgcgcattgggtcaccggtcacccgtcgccacaaccaactcggtggggtccgatgctgtctgatggcgcctcgcggcgaccaaccttatgagctaagggaagtcacaaactcacacgaacaataaagtgggatatacatgctcgcaagagtcaggaaaatacaatggcttggagtgatgttagtgataaaaatgaatcagatggatgaaggtgctgaacccactttttgttctcttttcgagattactctatacatacaacctcagctgcaagtttatcggaaaaatgatcaaaacttgacataaatatcgaaaaaacctcaattgtcaatgtaactcagtgtaatgtttcgataagcaacaatcgttgctgattgaatttttcaaataagtggcatagagattgaagtatcgttaaaaatagatcaagaaagatacaatgagttattttgagtcattggaaggtcattgatgtaaaagatgatcaagcgaagtaaaatatggtaccgacgacttttcacaaactgatcaagaaaagaggattgtaaaactttcgacacagcgtggacaaagataaacaacaggaattgcttatgtctcttagatctcaagggaaagagaaaaaaaaaagcaagctgtgacatgatgggatcaatgagtttggccttgaaagtcgtgttttagatagagcttgtcgtatcttttagctagtctcctacaaatgaataaatccccatttcaaaagtggcattcttagtcagctggcctcatagtggcttgaagtttttcttggaggtgaagagacccttcaaggaaggtcgagacagtctgctgttgtagcgagaggtgacatgttgagataagagggacactcacattttctgaaaaaggcccagcgcattttgtgcttccaaagtttccaaaaagatttactcgtcaaagcagctatcatttccctacaccaaatcgagaatctgtaaaaatgcgtttgggtgtggtgcttggcttgacgcaaccgagacttggcagccaaccaccaaagttgacgttttggtatcccattatacttgtgacatttcttattagaatgacctcgttttactagtgttctttgttgtcgtccggtcattgtccgggattgaacgagactggtctccatgctttctcgctctctcaaacaatatatgagaagagcagcttcctcttcggcctcctctgagtcaacatcatcatttgctaagtcaaccctattggtttctacgattgaattctgggtcgaagaggttctttccaagggacctaatttcagctcatctcccgcttcttcgcccatggtaccggtttccttgttcccgagcgcgagcgtctttatggactctaagtcgtggattccattttctactccaactgggccatgtgcgacgcccccaatgccatgaagaggtattaaaagaaagatcaagtaaaatgggagatgcatgatttcttcactacttgtgagtaattttaaagttctcaaagggtgatggatggcaagatgaatgcaatctctcctccggcaaagattccaaggatgactgaaggttttatattgtttactccggagattgtgaggtacctgcgcagccgaatctagagctgcactgccttttgcttacttgtacgatagtcacatacacgactgtgaacactgacttcgcgcaaacatgaaagatactctccctaccacacaaggccatcgacgttctccaaatgtgtcggcgtctcaggtgatgtagaagcggggcatctcgtagatagtgccgtcatacggtgcaagaaaccctctgctgtgaagatagtggggaaatgtgggcggtcgcatcggaggtggcaagttgtgatcccttcaaactctcaatatatcaaagtgtccgaacaaccacgcggcaaaactgaccatgacttagcttgcaatcgggtgacgaaatcaaaatctcgtcatgctgacgttctgaatacgtatcctcaagttcgcgtgcaggcctgcacaggctcagtcgtcgtcacatacacaagtactgtgaacactgacctcgcgcagacatgacagatagcctgcctacaacgaggctatggaggttctgcgagttgaccggcgtctcaagtagtgtagtcacggagcgatgcaaggcataacctctgatgtggtaatagggggtcaaattttcgtggtcggatccagggtggcaagttgtgatcatttcaaactcatattagagtattgagactccgaacaaccgcaccacaaaaccaagacggccggcacgagtgtctctactaatcttacggtaatacgtagtctttcgttcaagcagcgttacctcttgactgtatgaatgtataattcagtaattctggttcaattttaatcagcatatgggaggacttccggccgatctgtaggatcagatctagacccccctggaaattgatttttccgggggcatctggttctgaggcaggcaaatctgactctgtaagggctgccaagggctacagaaaatgacgagaagtcctccattacatacgacatacaagtaatcaaacatatggcttactagagatcaattttacccaagaatacaaa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data/test/data/PST130_7067.fa.fai

@@ -0,0 +1 @@
+PST130_7067	26091	13	26091	26092

data/test/data/PST130_reverse_primer.csv

@@ -0,0 +1 @@
+PST130_7067,T,3334,G,7067

data/test/data/Test3Aspecific.csv

@@ -1 +1,2 @@
-BS00183592,3A,TTGATCTCATAGAAGATGTAACAGCTCAGTTGCCTCCCAGCAAGGTGCCCCGTCTTCACTGTTTGGTGTGGCGAAAGTTATCATCTGTTGATTTTCTAGC[A/C]AAGTGTCCTGCTGTTGAGCCTTCACCAAGTCTCCTAAAAGGCATCCGGCAATCTTTGGTCTCACATCTCACTCTGGTATTAGGGAAAGATGACCTGGCAG
+BS00183592,3A,TTGATCTCATAGAAGATGTAACAGCTCAGTTGCCTCCCAGCAAGGTGCCCCGTCTTCACTGTTTGGTGTGGCGAAAGTTATCATCTGTTGATTTTCTAGC[A/C]AAGTGTCCTGCTGTTGAGCCTTCACCAAGTCTCCTAAAAGGCATCCGGCAATCTTTGGTCTCACATCTCACTCTGGTATTAGGGAAAGATGACCTGGCAG
+BS00183591,3A,TTGATCTCATAGAAGATGTAACAGCTCAGTTGCCTCCCAGCAAGGTGCCCCGTCTTCACTGTTTGGTGTGGCGAAAGTTATCATCTGTTGATTTTCTAGCgAAGTGTCCTGCTGTTGAGCCTTCACCAAGTCTCCTAAAAGGCATCCGGCAATCTTTGGTCTCACATCTCACTCTGGTATTAGGGAAAGATGACCTGGCAG

data/test/data/primer_3_input_header_test

@@ -0,0 +1,5 @@
+PRIMER_PRODUCT_SIZE_RANGE=50-200
+PRIMER_MAX_SIZE=25
+PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
+PRIMER_LIBERAL_BASE=1
+PRIMER_NUM_RETURN=5

data/test/test_snp_parsing.rb

@@ -33,6 +33,7 @@ class TestPolyploidTools < Test::Unit::TestCase
     assert_equal(snp.position ,  51, "Position isnt parsed #{snp.position}")
     assert_equal(snp.original , "T", "ORiginal base not parsed, is #{snp.original}")
     assert_equal(snp.snp , "C")
+    
     assert(snp.template_sequence == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA", "#{snp.template_sequence}!=CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
     #true
   end

data/test/test_wrong_selection.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+test_out=$DIR/test_out
+rm -rf $test_out
+$DIR/../bin/polymarker.rb -c $DIR/data/PST130_7067.fa -s  $DIR/data/PST130_7067.csv -r $DIR/data/PST130_7067.fa  -o $test_out -e affine:local -a arm_selection_morex

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.3.3
+  version: 0.4.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-30 00:00:00.000000000 Z
+date: 2014-09-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -94,6 +94,7 @@ executables:
 - map_markers_to_contigs.rb
 - markers_in_region.rb
 - polymarker.rb
+- snp_position_to_polymarker.rb
 - snps_between_bams.rb
 extensions: []
 extra_rdoc_files:
@@ -116,6 +117,7 @@ files:
 - bin/map_markers_to_contigs.rb
 - bin/markers_in_region.rb
 - bin/polymarker.rb
+- bin/snp_position_to_polymarker.rb
 - bin/snps_between_bams.rb
 - bio-polyploid-tools.gemspec
 - conf/defaults.rb
@@ -178,12 +180,17 @@ files:
 - test/data/LIB1721.bam.bai
 - test/data/LIB1722.bam
 - test/data/LIB1722.bam.bai
+- test/data/PST130_7067.csv
+- test/data/PST130_7067.fa
+- test/data/PST130_7067.fa.fai
+- test/data/PST130_reverse_primer.csv
 - test/data/S22380157.fa
 - test/data/S22380157.fa.fai
 - test/data/Test3Aspecific.csv
 - test/data/Test3Aspecific_contigs.fa
 - test/data/bfr_out_test.csv
 - test/data/patological_cases5D.csv
+- test/data/primer_3_input_header_test
 - test/data/short_primer_design_test.csv
 - test/data/test_primer3_error.csv
 - test/data/test_primer3_error_contigs.fa
@@ -191,6 +198,7 @@ files:
 - test/test_exon_container.rb
 - test/test_exonearate.rb
 - test/test_snp_parsing.rb
+- test/test_wrong_selection.sh
 homepage: http://github.com/tgac/bioruby-polyploid-tools
 licenses:
 - MIT