bio-polyploid-tools 0.4.7 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a8d3e6e4da66e6557537f1ee0a51482254f40d5d
-  data.tar.gz: 581f159c41f099ce1f3ab9f177b091e686edb535
+  metadata.gz: b72bd3369d361c595f7709f9afad4e6c7c815dcc
+  data.tar.gz: 9e7feca5269cba60eb49725c1954d55c63bf8f9b
 SHA512:
-  metadata.gz: 280f1db971fa149cf9a6eb901a11f3fc26f6b5ff11340495878931bdf1384bcb4345d9b465d8a6763f12ff7c8bba9a4b8ffa7e34737d2882fd3382f0a7c75383
-  data.tar.gz: 0220f04966b2dd0874fcdb94baab552e142265896ed85acc36401a8e18d7833360d02c172fdb0e878e7793765bf6c05022e11ee62bae89336842e5040574279f
+  metadata.gz: 5e74d4df3e6f04f6dc884521a5470d97a59013168ab2c3978658d8c498d5a499ae8a72abf014d45939b1f366f387608d52f09dccc0fc2715132f63be9059c51a
+  data.tar.gz: 745042ade686bfa72436c6b9db555e032350ef4f868f95fe548ee0a02f0279628db71e04630b29e2b80c53c8b791f72d3fbfc276af9357036f425eeedf3ed80c

data/VERSION

@@ -1 +1 @@
-0.4.7
+0.5.0

data/bin/polymarker.rb

@@ -35,19 +35,17 @@ options[:bucket_size] = 0
 options[:bucket] = 1
 options[:model] = "est2genome"
 options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
-options[:flanking_size] = 100;
+options[:flanking_size] = 150;
 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_explain_flag => 1,
       :primer_thermodynamic_parameters_path=>File.expand_path(File.dirname(__FILE__) + '../../conf/primer3_config/') + '/'
-
     }
 
-
-
 OptionParser.new do |opts|
   opts.banner = "Usage: polymarker.rb [options]"
 
@@ -81,6 +79,7 @@ OptionParser.new do |opts|
   
   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!
@@ -214,12 +213,12 @@ target=filename
 fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
 fasta_file.load_fai_entries
 
-found_cointigs = Set.new
+found_contigs = Set.new
 Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model}) do |aln|
   if aln.identity > min_identity
     exo_f.puts aln.line
-    unless found_cointigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file. 
-      found_cointigs.add(aln.target_id)
+    unless found_contigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file. 
+      found_contigs.add(aln.target_id)
       entry = fasta_file.index.region_for_entry(aln.target_id)
       raise ExonerateException.new,  "Entry not found! #{aln.target_id}. Make sure that the #{target_id}.fai was generated properly." if entry == nil
       region = entry.get_full_region
@@ -259,12 +258,6 @@ 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}/")
 
 Bio::DB::Primer3.prepare_input_file(file, options[:primer_3_preferences])
 added_exons = container.print_primer_3_exons(file, nil, snp_in)
@@ -284,7 +277,7 @@ snps.each do |snp|
 end
 
 kasp_container.add_primers_file(primer_3_output) if added_exons > 0
-header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size"
+header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
 
 write_status "DONE"

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 0.4.7 ruby lib
+# stub: bio-polyploid-tools 0.5.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.4.7"
+  s.version = "0.5.0"
 
   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 = "2014-10-09"
+  s.date = "2014-10-14"
   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

@@ -136,12 +136,13 @@ module Bio::PolyploidTools
           begin 
             primer_3_min_seq_length
             string = snp.primer_3_string( snp.chromosome, parental )
+            #puts "print_primer_3_exons: #{string.size}"
             if string.size > 0
               file.puts string
               added += 1
             end 
            rescue Exception=>e
-             @missing_exons << snp.to_s
+              @missing_exons << snp.to_s
 
               $stderr.puts e.to_s
             end

data/lib/bio/db/primer3.rb

@@ -22,9 +22,9 @@ module Bio::DB::Primer3
       :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/') + '/'
-
+      :primer_num_return => 5,
+      :primer_explain_flag => 1,
+      :primer_thermodynamic_parameters_path => File.expand_path(File.dirname(__FILE__) + '../../../../conf/primer3_config/') + '/'
     }.merge(opts2)
     
     opts.each do |key,value|
@@ -67,7 +67,8 @@ module Bio::DB::Primer3
     def initialize
       @primers_line_1 = SortedSet.new
       @primers_line_2 = SortedSet.new
-      @reguibs = SortedSet.new
+      @regions = SortedSet.new
+       @primer3_errors = Set.new
     end
 
     def line_2_name
@@ -112,11 +113,7 @@ module Bio::DB::Primer3
       left_end = 0
       right_start = 0
       right_end = 0
- #     exons = snp_from.exon_list.values
-      
-#      puts "Exons: #{exon_list.size}"
-      
-#      puts "It has the following exons: #{snp_in.exon_list.to_s}"
+      total_columns_before_messages=17
       values = Array.new
       #values << "#{gene},,#{template_length},"
       values << gene
@@ -242,6 +239,12 @@ module Bio::DB::Primer3
         values << primer3_line_2.best_pair.product_size
 
       end 
+      if values.size < total_columns_before_messages
+        values[total_columns_before_messages] = primer3_errors.to_a.join("|")
+      else
+        values << nil
+      end
+
       values.join(",")
     end
 
@@ -268,13 +271,14 @@ module Bio::DB::Primer3
 
     
     def add_record(primer3record)
-      @primer3_errors = Array.new unless @primer3_errors
+      @primer3_errors = Set.new unless @primer3_errors
       @template_length = primer3record.sequence_template.size
        if primer3record.primer_error != nil 
-          primer3_errors << primer3record
+          primer3_errors << primer3record.primer_error
           return
         end
       case
+
       when primer3record.line == @line_1
 
         @line_1_template = primer3record.sequence_template
@@ -297,6 +301,10 @@ module Bio::DB::Primer3
         else
           raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
         end
+      else
+        primer3_errors << "#{primer3record.line}(#{primer3record.orientation}):#{primer3record.primer_left_explain}"
+        primer3_errors << "common(#{primer3record.orientation}#{primer3record.type}):#{primer3record.primer_right_explain}"
+        primer3_errors << "pair(#{primer3record.orientation}#{primer3record.type}):#{primer3record.primer_pair_explain}"
       end
     end
   end
@@ -327,7 +335,8 @@ module Bio::DB::Primer3
       return @properties[method_name] if @properties[method_name] 
       $stderr.puts "Missing #{method_name}"
       $stderr.puts @properties.inspect
-      raise NoMethodError.new() 
+      return "" #if a property is missing, return blank. 
+      #raise NoMethodError.new() 
     end
 
     def find_left_tm(primer)
@@ -665,26 +674,18 @@ module Bio::DB::Primer3
       snp.position = snp_in.position
       snp.snp = snp_in.snp
 
-#      snp.original.upcase!
-#      snp.snp.upcase! 
       snp.line_1 = @line_1
       snp.line_2 = @line_2 
       snp.snp_from = snp_in
-      #puts "Kasp container, adding #{snp.to_s} #{snp.class}  #{snp_in.class}"
-      #puts "#{snp.regions}"
       snp.regions = snp_in.exon_list.values.collect { |x| x.target_region.to_s }
-      #puts "#{snp.regions}"
       @snp_hash[snp.to_s] = snp
       snp
     end
 
     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)
-
       end
     end
 
@@ -695,8 +696,6 @@ module Bio::DB::Primer3
       end
       return str
     end
-
   end
-
 end
 

data/test/data/test_iselect.csv

@@ -98,7 +98,6 @@ RAC875_c9500_1796,2B,TTGCCCATGACACAGCTAGATTCTGTCACCTCAATCTTTGTAATCTCATC[A/G]TCTT
 RAC875_c95103_67,7A,GTGTGCATGTTGGATGGTCACATTCTAGTGTACTAGCTAGCTAGTAAGCT[T/G]GTTTTGCTACCGGATGATTGAATGTCATCTCAGTTTGTACCTCATCTAGC
 RAC875_c9523_328,2A,TCGGCGTGTTGATCCTGGAGATCGTGTGTGGCCGTAGGAACAGCTCCCTC[A/G]ttgatcacgaatggtcaatgaaccttgtgggccacgcatggacgctgtgg
 RAC875_c9542_235,7A,TATTTCATCCGAGCAGGGAGAAATGCCAGTAGTTCAATATTGCCAGATGG[T/G]CAACTGTCTTATTAGGATGGAATCCCGTCCGTATAAGATTGGTGGTTCCT
-RAC875_c9543_99,2A,CGGAGTAAATATATGAAACACAACGGGGAACTTGTGTTTGCTAAAATGAT[T/G]GAGCGACTACTCTGCTTTGAATATATGCAGGGCGGAAGCCTTGAGAAATA
 RAC875_c9543_99,7B,CGGAGTAAATATATGAAACACAACGGGGAACTTGTGTTTGCTAAAATGAT[T/G]GAGCGACTACTCTGCTTTGAATATATGCAGGGCGGAAGCCTTGAGAAATA
 RAC875_c95993_265,3B,GCGGCTCCATGGAAGCCGCCATCATGTTGTCCGACTAAATGTGGAGTTAC[T/C]TGTGCAAGTTCCACCATCAACAAACACAAAGTTCTGCATGCTATCATCGC
 RAC875_c9601_1680,1D,CTGATGAACCAGAATGCCCATTCCTTATGAAGCGTGGGTACTGTAAACTT[A/C]gggcacaatgtaagttttatcacccagaggcttcgagcccaacagatgca
@@ -119,7 +118,6 @@ RAC875_c982_710,6B,TGGGAGCCATAGTTGTTTGGGCAGGAGCAAAATGCCTTTGTGATGGTCGA[T/G]AGCTGG
 RAC875_c98608_173,5B,CTACAGAAGATGAGATCGTCGCTGCAGACGGTGGAGGCCCTGCTCGAAGA[T/C]GCTGAGAGGCGGTCCATCACGGATCAGGCGGTGCGTCTGTGGCTGGGGCG
 RAC875_c98794_101,3D,cataaatcgtcatacatatagagaggggaatccagggcaatctcagggtt[A/G]GGGAGCAATCCAGCAATGATCACCAGCACCTGAAAGTACCATGTCTCAAG
 RAC875_c99286_60,6A,GCAGATTAAGGTCAGAGGAAGCATCTGCTACGAGGAACATCTTCGTCTTC[A/G]ACCTACAGGTGGAATATGCAGAGCAAGCACGGGCGTGCATCCGTGCCGCC
-RAC875_c99286_90,2A,CGAGGAACATCTTCGTCTTCAACCTACAGGTGGAATATGCAGAGCAAGCA[T/C]GGGCGTGCATCCGTGCCGCCTTGGGTAGCCACCCCAGATTCGTCGTGCCC
 RAC875_c99286_90,6A,CGAGGAACATCTTCGTCTTCAACCTACAGGTGGAATATGCAGAGCAAGCA[T/C]GGGCGTGCATCCGTGCCGCCTTGGGTAGCCACCCCAGATTCGTCGTGCCC
 RAC875_c9932_705,2B,TGCCGATGCAGATGTCCAGCAATGATAAGGTTGCTACGCTCAAAGAACAA[T/C]GGATGGTACATAAGCGAGCACAGGGAATTCCACAACCACTCTCTTACAGA
 RAC875_c9934_252,5A,TAGAGTCGGACGCGTCGTGATGGCCGCAGCGGCCAAGCATCTGACGCCGG[T/C]CGTCTTGGAGCTCGGTGGCAAATGCCCGGTGGTTGTCGATTCAAACGTCG
@@ -184,7 +182,6 @@ RAC875_rep_c106158_701,4A,AATGATGAGAGCTCTAATTTTATCAACTCACTAGACACCATGACCACTCC[T/G
 RAC875_rep_c106170_204,3D,GAAATCTTTTATGTCCCCCAGCGACCATATACAGCTGTCGGAACACTTCG[T/C]GACCAGTTAATCTATCCACTTACAGCAGATCAGGAAACCGAACCACTTAG
 RAC875_rep_c106177_206,4B,ATTTGCATGGTCTATGGTGGCATCAATTGCACCATCTCTTATGGCCTTGG[T/C]TACGATGCACTCCGCATCAGCAACAGGATTCTCAGTGTCTAGCCTTAGCT
 RAC875_rep_c106241_304,5A,ATGATCCTTCCTACTGGAGCTGCCTCATTCAAGGAGGCAATGAAGATGGG[T/C]gttgaagtgtaccacaacttgaagtctgttatcaagaagaagtatgggca
-RAC875_rep_c106241_304,5B,ATGATCCTTCCTACTGGAGCTGCCTCATTCAAGGAGGCAATGAAGATGGG[T/C]gttgaagtgtaccacaacttgaagtctgttatcaagaagaagtatgggca
 RAC875_rep_c106322_1091,4B,TGAACTTCCCAAGATCACGAAGTGCTATAGTTTTGAGATATATGGTCTCC[A/G]TTACTAGATTAACAGTATGCAAGGACATTGGTGGATAACTGGAATGTGGA
 RAC875_rep_c106400_276,2B,CCCGATCTTTGCATCGACACGATCACAAAGAACCGAACAGGATTACACGA[A/G]cattccgccctgctgtaaccctttggctttgggaagtgcacgtagggcag
 RAC875_rep_c106488_130,5A,CTTGCGTTAGTCTCATGGCAGGCCACTGCTTCTGATCCTAGCCCACTCCA[A/G]gacttttgtgtcgccgacatgaattcaccagtccgtgtcaatgggtttgt
@@ -196,5 +193,4 @@ RAC875_rep_c106636_232,3A,CTTTAGGCATCGCCCGAGGAACGGAGTACCTGCATCAAGGTTGCAACCAG[T/C
 RAC875_rep_c106876_558,1B,ttatgatcagattaagaagatgaacaccttcggctattttctggtactta[T/C]TGCGCCTTGCATAATCTTCGTGATGAATGTGCTTTGGTTCTCCAAGATCC
 RAC875_rep_c106976_263,7A,ATCACCATCTCCCTGCTGTGGGTCGCCATCAACCCGCCGTCGCAGAACTC[A/G]CAGATCGGAGGCTCCTTCCAGTTCCCCTGATCGATGAAGCTAGCTTCCTC
 RAC875_rep_c107031_84,2B,AATTAGGTCTTGCAGCAGGCGCCCCACCTCCAGAATAGGAACTATGAGGT[T/G]GTTGCTGCTGCCACTGTTGGGCTCCTGCATATGGTGCAGGCTGGTAGACC
-RAC875_rep_c107110_137,3B,AAGAGATAATCACCGTGGCCAAGGCGGCCAACGCTCATGAGTTCATATCG[A/G]GCTTGCCACAGGGATACAACACTAACGTTGGTGAGAGAGGAACACAACTA
-RAC875_rep_c107110_137,3D,AAGAGATAATCACCGTGGCCAAGGCGGCCAACGCTCATGAGTTCATATCG[A/G]GCTTGCCACAGGGATACAACACTAACGTTGGTGAGAGAGGAACACAACTA
+RAC875_rep_c107110_137,3B,AAGAGATAATCACCGTGGCCAAGGCGGCCAACGCTCATGAGTTCATATCG[A/G]GCTTGCCACAGGGATACAACACTAACGTTGGTGAGAGAGGAACACAACTA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.4.7
+  version: 0.5.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-09 00:00:00.000000000 Z
+date: 2014-10-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio