bio-polyploid-tools 0.8.4 → 0.8.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 728d9fb436e9e7d26698d011179da63ba79fc45c40b0a771cafc5f4dc6d84bc3
-  data.tar.gz: 3c62bd8bcfcb5d3f460729f19f8382bd46c7821fcacb83d01b0ff3f336b38f1b
+  metadata.gz: 1f13bb3db0a9396fa0468962dd23f34a771c6772a613f873dd3728cb47f66204
+  data.tar.gz: d5427afc0216c123131894858aeb8d8ddd0eed53c47b4e47d4b34e63d67af1f2
 SHA512:
-  metadata.gz: 99784b38c37f00e71c3c1fa07899ccca8e32b6ff27fc363bcece989e788c0db745a7db4ae566efb42b55742fd01e5a99adeb211a7d46029f6c148dba8e91e92a
-  data.tar.gz: 40f0990a5652374ea3bef3b0e8777882720626e33fdc448ff48c5f71141b87ce153680a0215ad95e13595ddead39db822d276911baf0647723cc7e8bf3195bdb
+  metadata.gz: '01730361649ede299bc462eda6e9f92c7882aa13ee98033f5276268971efd7a7c03d617ecd089276d2c296e0ff842bd51395839f9134626a6f2bfd7b31840b58'
+  data.tar.gz: 24c571c5a9318bdd56d8cac17ba008e5b3c22877042bba1198e2d0d9dcbe4b32e330f0963696eca7cd820620166a81a62b8cfa0c0dccb51a34e9370d11bd3bea

data/README.md

@@ -128,6 +128,12 @@ To use blast instead of exonerate, use the following command:
 
 ## Release Notes
 
+### Next release
+
+### 0.8.5
+
+* Added the option ```--max_hits``` to ```polyamarker.rb``` to set a maximum number of bast hits to identify repetitive regions. This adds the column ```is_repetitve``` to the output. The mask is not calculated in repetitive regions and the primers are designed as non-specific. 
+
 ### 0.8.4 
 
 * Added script ```tag_stats.rb`` That gets the descriptive statistics for a tag in a bam file for each reference. 

data/VERSION

@@ -1 +1 @@
-0.8.4
+0.8.5

data/bin/blast_triads.rb

@@ -144,7 +144,7 @@ CSV.foreach(options[:triads], headers:true ) do |row|
     FileUtils.cp(b_tmp, save_folder) if seq_b
     FileUtils.cp(d_tmp, save_folder) if seq_d
    end
-
+   #This had a bug where the columns where always "AB"
    if seq_a and seq_b
       to_print = [triad, a, b , "A","B","A->B"]
       to_print << blast_pair_fast(a_tmp, b_tmp, out_tmp, program:options[:program])
@@ -152,13 +152,13 @@ CSV.foreach(options[:triads], headers:true ) do |row|
       puts to_print.join("\t")
    end
   if seq_a and seq_d
-      to_print = [triad, a, b , "A","D","A->D"]
+      to_print = [triad, a, d , "A","D","A->D"]
       to_print << blast_pair_fast(a_tmp, d_tmp, out_tmp, program:options[:program]) 
       puts to_print.join("\t")
       FileUtils.cp(out_tmp, "#{save_folder}/A_D.xml") if save
   end
   if seq_b and seq_d
-      to_print = [triad, a, b , "B","D","B->D"]
+      to_print = [triad, b, d , "B","D","B->D"]
       to_print << blast_pair_fast(b_tmp, d_tmp, out_tmp, program:options[:program])
       FileUtils.cp(out_tmp, "#{save_folder}/B_D.xml") if save
       puts to_print.join("\t")

data/bin/polymarker.rb

@@ -39,6 +39,7 @@ options[:min_identity] = 90
 options[:scoring] = :genome_specific
 options[:database]  = false
 options[:filter_best]  = false
+options[:max_hits] = 10
 options[:aligner] = :exonerate
 
 
@@ -57,68 +58,70 @@ options[:primer_3_preferences] = {
 OptionParser.new do |opts|
   opts.banner = "Usage: polymarker.rb [options]"
 
+  opts.on("-a", "--arm_selection #{Bio::PolyploidTools::ChromosomeArm.getValidFunctions.join('|')}", "Function to decide the chromome arm") do |o|
+    tmp_str = o
+    arr = o.split(",")
+    if arr.size == 2
+       options[:arm_selection] = lambda do |contig_name|
+          separator, field = arr
+          field = field.to_i
+          ret = contig_name.split(separator)[field]
+          return ret
+        end
+    else
+      options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection(o)
+    end
+   end
+
+  opts.on("-b", "--filter_best", "If set, only keep the best alignment for each chromosome") do 
+    options[:filter_best]  = true
+  end
+
   opts.on("-c", "--contigs FILE", "File with contigs to use as database") do |o|
     options[:path_to_contigs] = o
   end
   
-  opts.on("-m", "--marker_list FILE", "File with the list of markers to search from") do |o|
-    options[:marker_list] = o
+  opts.on("-d", "--database PREFIX", "Path to the blast database. Only used if the aligner is blast. The default is the name of the contigs file without extension.") do |o|
+    options[:database] = o
+  end
+
+  opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
+     options[:model] = o
   end
 
   opts.on("-g", "--genomes_count INT", "Number of genomes (default 3, for hexaploid)") do |o|
     options[:genomes_count] = o.to_i
   end
-  
-  opts.on("-b", "--filter_best", "If set, only keep the best alignment for each chromosome") do 
-    options[:filter_best]  = true
-  end
 
-
-  opts.on("-s", "--snp_list FILE", "File with the list of snps to search from, requires --reference to get the sequence using a position") do |o|
-    options[:snp_list] = o
+  opts.on("-i", "--min_identity INT", "Minimum identity to consider a hit (default 90)") do |o|
+    options[:min_identity] = o.to_i
   end
 
-  opts.on("-t", "--mutant_list FILE", "File with the list of positions with mutation and the mutation line.\n\
-    requires --reference to get the sequence using a position") do |o|
-    options[:mutant_list] = o
-  end
-  
-  opts.on("-r", "--reference FILE", "Fasta file with the sequence for the markers (to complement --snp_list)") do |o|
-    options[:reference] = o
+  opts.on("-m", "--marker_list FILE", "File with the list of markers to search from") do |o|
+    options[:marker_list] = o
   end
 
-  opts.on("-i", "--min_identity INT", "Minimum identity to consider a hit (default 90)") do |o|
-    options[:min_identity] = o.to_i
-  end
-  
   opts.on("-o", "--output FOLDER", "Output folder") do |o|
     options[:output_folder] = o
   end
-  
-  opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
-     options[:model] = o
-  end
-
-  opts.on("-a", "--arm_selection #{Bio::PolyploidTools::ChromosomeArm.getValidFunctions.join('|')}", "Function to decide the chromome arm") do |o|
-    tmp_str = o
-    arr = o.split(",")
-    if arr.size == 2
-       options[:arm_selection] = lambda do |contig_name|
-          separator, field = arr
-          field = field.to_i
-          ret = contig_name.split(separator)[field]
-          return ret
-        end
-    else
-      options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection(o)
-    end
 
-   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
 
+  opts.on("-r", "--reference FILE", "Fasta file with the sequence for the markers (to complement --snp_list)") do |o|
+    options[:reference] = o
+  end
+  
+  opts.on("-s", "--snp_list FILE", "File with the list of snps to search from, requires --reference to get the sequence using a position") do |o|
+    options[:snp_list] = o
+  end
+
+  opts.on("-t", "--mutant_list FILE", "File with the list of positions with mutation and the mutation line.\n\
+    requires --reference to get the sequence using a position") do |o|
+    options[:mutant_list] = o
+  end
+  
   opts.on("-v", "--variation_free_region INT", "If present, avoid generating the common primer if there are homoeologous SNPs within the specified distance") do |o|
     options[:variation_free_region] = o.to_i
   end
@@ -127,23 +130,24 @@ OptionParser.new do |opts|
     options[:extract_found_contigs] = true
   end
 
-  opts.on("-P", "--primers_to_order", "If present, save a separate file with the primers with the KASP tails")do
-    #TODO: have a string with the tails, optional. 
-    options[:primers_to_order] = true
+  opts.on("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: exonerate") do |o|
+    raise "Invalid aligner" unless o == "exonerate" or o == "blast" 
+    options[:aligner] = o.to_sym
   end
 
   opts.on("-H", "--het_dels", "If present, change the scoring to give priority to: semi-specific, specific, non-specific")  do
     options[:scoring] = :het_dels
   end
 
-  opts.on("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: exonerate") do |o|
-    raise "Invalid aligner" unless o == "exonerate" or o == "blast" 
-    options[:aligner] = o.to_sym
+  opts.on("-M", "--max_hits INT", "Maximum number of hits to consider a region as non repetitive. Markers with more than this number of hits will be ignored. (default #{options[:max_hits]})") do |o|
+    options[:max_hits] = o.to_i
   end
 
-  opts.on("-d", "--database PREFIX", "Path to the blast database. Only used if the aligner is blast. The default is the name of the contigs file without extension.") do |o|
-    options[:database] = o
+  opts.on("-P", "--primers_to_order", "If present, save a separate file with the primers with the KASP tails")do
+    #TODO: have a string with the tails, optional. 
+    options[:primers_to_order] = true
   end
+
 end.parse!
 
 
@@ -308,7 +312,7 @@ 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}) do |aln|
+Bio::DB::Blast.align({:max_hits=>options[:max_hits], :query=>temp_fasta_query, :target=>options[:database], :model=>model}) do |aln|
   do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options)
 end if options[:aligner] == :blast
 
@@ -329,8 +333,9 @@ contigs_f.close() if options[:extract_found_contigs]
 write_status "Reading best alignment on each chromosome"
 
 
-container= Bio::PolyploidTools::ExonContainer.new
-container.flanking_size=options[:flanking_size] 
+container = Bio::PolyploidTools::ExonContainer.new
+container.flanking_size = options[:flanking_size] 
+container.max_hits = options[:max_hits]
 container.gene_models(temp_fasta_query)
 container.chromosomes(target)
 container.add_parental({:name=>snp_in})
@@ -387,7 +392,7 @@ 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,errors"
+header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,is_repetitive,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}") }
 
 File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails()) }

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 0.8.4 ruby lib
+# stub: bio-polyploid-tools 0.8.5 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.8.4"
+  s.version = "0.8.5"
 
   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 = "2018-02-27"
+  s.date = "2018-07-31"
   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, "find_homoeologue_variations.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, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze]
@@ -151,6 +151,8 @@ Gem::Specification.new do |s|
     "test/data/Test3Aspecific.csv",
     "test/data/Test3Aspecific_contigs.fa",
     "test/data/bfr_out_test.csv",
+    "test/data/chr4D_C14473543T/chr4D_C14473543T.csv",
+    "test/data/chr4D_C14473543T/chr4D_C14473543T.fa",
     "test/data/headerMergeed.txt",
     "test/data/headerS2238015",
     "test/data/mergedLibs.bam",

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 , :primer_3_min_seq_length
+    attr_accessor :flanking_size , :primer_3_min_seq_length, :max_hits
 
     BASES = [:A, :C, :G, :T]
     #Sets the reference file for the gene models
@@ -15,6 +15,7 @@ module Bio::PolyploidTools
       @snp_map = Hash.new 
       @snp_contigs
       @primer_3_min_seq_length = 50
+      @max_hits = 10
     end
 
     def gene_models(path)
@@ -76,8 +77,11 @@ module Bio::PolyploidTools
     end
     
     def add_snp(snp)
+      #TODO: add to the snp the maximum number of hits? 
+      snp.max_hits = self.max_hits
       @snp_map[snp.gene] = Array.new unless   @snp_map[snp.gene] 
       @snp_map[snp.gene] << snp
+
     end
 
     def add_snp_file(filename, chromosome, snp_in, original_name)
@@ -157,6 +161,7 @@ module Bio::PolyploidTools
           begin 
             primer_3_min_seq_length
             string = snp.primer_3_string( snp.chromosome, parental )
+            #TODO: add tan error to the SNP this snp has more than max_hits. Or maybe inside the SNP file. 
             #puts "print_primer_3_exons: #{string.size}"
             if string.size > 0
               file.puts string
@@ -208,6 +213,20 @@ module Bio::PolyploidTools
           end
         end
       end
+      remove_alignments_over_max_hits
+    end
+
+    def remove_alignments_over_max_hits
+      @snp_map.each_pair do | gene, snp_array| 
+        snp_array.each do |snp|
+          if snp.exon_list.size > max_hits
+            total_hits = snp.exon_list.size
+            snp.exon_list = {} 
+            snp.repetitive = true
+            snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"
+          end
+        end
+      end
     end
 
     def add_parental(opts=Hash.new) 

data/lib/bio/PolyploidTools/SNP.rb

@@ -15,6 +15,9 @@ module Bio::PolyploidTools
     attr_accessor :primer_3_min_seq_length 
     attr_accessor :chromosome
     attr_accessor :variation_free_region
+    attr_accessor :max_hits
+    attr_accessor :errors
+    attr_accessor :repetitive
 
 
 
@@ -62,7 +65,10 @@ module Bio::PolyploidTools
       @primer_3_min_seq_length = 50
       @variation_free_region = 0
       @contig = false
+      @max_hits = 10
       @exon_list = Hash.new {|hsh, key| hsh[key] = [] }
+      @errors = Array.new
+      @repetitive = false
     end
 
     def to_polymarker_coordinates(flanking_size, total:nil)
@@ -329,11 +335,17 @@ module Bio::PolyploidTools
       primer_3_propertes = Array.new
 
       seq_original = String.new(pr.sequence)
-      #puts seq_original.size.to_s << "-" << primer_3_min_seq_length.to_s 
-      return primer_3_propertes if seq_original.size < primer_3_min_seq_length
-      #puts self.inspect
-      #puts pr.snp_pos.to_s << "(" << seq_original.length.to_s << ")"
       
+      if seq_original.size < primer_3_min_seq_length
+        errors << "The sequence (#{seq_original.size}) is shorter than #{primer_3_min_seq_length}"
+        return primer_3_propertes 
+      end
+
+      if exon_list.size > max_hits
+        errors << "The marker maps to #{exon_list.size} positions (max_hits: #{max_hits}). "
+        repetitive = true
+        return primer_3_propertes 
+      end
       seq_original[pr.snp_pos] = self.original
       seq_original_reverse = reverse_complement_string(seq_original)
 

data/lib/bio/db/blast.rb

@@ -79,7 +79,9 @@ module Bio::DB::Blast
 	def self.align(opts={})
 		target=opts[:target]
 		query=opts[:query]
-		cmdline = "blastn -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
+		max_target_seqs = 15
+		max_target_seqs = opts[:max_hits] + 1 if opts[:max_hits]
+		cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
 
 		status, stdout, stderr = systemu cmdline
 		if status.exitstatus == 0

data/lib/bio/db/primer3.rb

@@ -59,6 +59,7 @@ module Bio::DB::Primer3
     attr_accessor :snp_from
     attr_accessor :regions
     attr_accessor :primer3_errors
+    attr_accessor :repetitive
     
     def line_1_name
       "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
@@ -112,7 +113,7 @@ module Bio::DB::Primer3
       left_end = 0
       right_start = 0
       right_end = 0
-      total_columns_before_messages=17
+      total_columns_before_messages=18
       #puts "Values in primer3"
       #puts snp_from.inspect
       @values = Array.new
@@ -123,6 +124,7 @@ module Bio::DB::Primer3
       @values << snp_from.chromosome
       @values << regions.size
       @values << regions.join("|")
+      @values << repetitive
       if primer3_line_1 and primer3_line_2
         @values <<  primer3_line_1.polymorphism
 
@@ -655,8 +657,7 @@ module Bio::DB::Primer3
       @values = Hash.new
     end
 
-    def method_missing(m, *args, &block)  
-
+    def method_missing(m, *args, &block)
       return @values[m.to_s] if @values[m.to_s] != nil
       raise NoMethodError.new(), "There's no method called #{m}, available: #{@values.keys.to_s}."  
     end
@@ -754,13 +755,15 @@ module Bio::DB::Primer3
     end
 
     def add_snp(snp_in) 
+      #TODO: Here we need to also copy the errors that will be printed. 
       @snp_hash=Hash.new unless @snp_hash
       snp = SNP.new
       snp.gene = snp_in.gene
       snp.original = snp_in.original
-
+      snp.primer3_errors = Set.new snp_in.errors
       snp.position = snp_in.position
       snp.snp = snp_in.snp
+      snp.repetitive = snp_in.repetitive
 
       snp.line_1 = @line_1
       snp.line_2 = @line_2 

data/test/data/chr4D_C14473543T/chr4D_C14473543T.csv

@@ -0,0 +1 @@
+Chr4D_C14473543T,4D,AACCAGTGTAAACCTTGTGTCCCTTGTTCTTCGGGCTCGACGCGCTAAGCCTTGAGATCGCGGTTTGGGCGTGAGTTAGGGAAGAGAGAGATCTTCGTGC[C/T]CACCCCAGAGTTCGAACCTTAAGGGTTTTGCCGAAACCCGAAATCCGACAATTGTGATGAAAGTTGAGCTCCTCGGTAGCCTTGACTCCGGGAACAAGCT

data/test/data/chr4D_C14473543T/chr4D_C14473543T.fa

@@ -0,0 +1,2 @@
+>chr4D_C14473543T
+aaccagtgtaaaccttgtgtcccttgttcttcgggctcgacgcgctaagccttgagatcgcggtttgggcgtgagttagggaagagagagatcttcgtgcYcaccccagagttcgaaccttaagggttttgccgaaacccgaaatccgacaattgtgatgaaagttgagctcctcggtagccttgactccgggaacaagct

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.8.4
+  version: 0.8.5
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-02-27 00:00:00.000000000 Z
+date: 2018-07-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -271,6 +271,8 @@ files:
 - test/data/Test3Aspecific.csv
 - test/data/Test3Aspecific_contigs.fa
 - test/data/bfr_out_test.csv
+- test/data/chr4D_C14473543T/chr4D_C14473543T.csv
+- test/data/chr4D_C14473543T/chr4D_C14473543T.fa
 - test/data/headerMergeed.txt
 - test/data/headerS2238015
 - test/data/mergedLibs.bam