bio-polymarker 1.3.2

data/lib/bio/PolyploidTools/Mask.rb

@@ -0,0 +1,116 @@
+require 'bio'
+
+class Array
+  def sum
+    inject(0.0) { |result, el| result + el }
+  end
+
+  def mean
+    sum / size
+  end
+end
+
+module Bio::PolyploidTools::Mask
+  def self.find_end(seqs)
+    size = seqs.values[0].size
+    names = seqs.keys
+    i = size - 1
+    gap_count = 3
+    while i > 0 and gap_count > 0
+      gap_count = names.map { |chr| seqs[chr][i] == "-" ? 1:0  }.inject(0, :+)
+      i -= 1
+    end
+    i + 1
+  end
+
+  def self.find_start(seqs)
+    size = seqs.values[0].size
+    names = seqs.keys
+    i = 0
+    gap_count = 3
+    while i < size  and gap_count > 0
+      gap_count = names.map { |chr| seqs[chr][i] == "-" ? 1 : 0  } .inject(0, :+)
+
+      i += 1
+    end
+    i - 1
+  end
+
+  def self.get(seqs, target: nil, seq_start: 0, seq_end: 0)
+    names = seqs.keys
+    target = names[0] if target.nil?
+    masked_snps = seqs[target].downcase
+    i = 0
+    while i < masked_snps.size
+      different = 0
+      cov = 0
+      gap = false
+      names.each do | chr |
+        if seqs[chr][i]  != "-" and seqs[chr][i]  != "n" and seqs[chr][i]  != "N"
+          cov += 1
+        end
+        if chr != target
+         different += 1  if masked_snps[i].upcase != seqs[chr][i].upcase
+        end
+        if seqs[chr][i]  == "-" and chr == target
+            gap = true
+        end
+      end
+      masked_snps[i] = "." if different == 0
+      masked_snps[i] = "." if cov == 1
+      masked_snps[i] = "*" if cov == 0
+      expected_snps  = names.size - 1
+      masked_snps[i] = masked_snps[i].upcase if different == expected_snps
+      if gap
+        masked_snps[i] = different == expected_snps ? "-" : "_"
+      end
+      masked_snps[i] = "|" if i < seq_start or i > seq_end
+      i += 1
+    end
+    masked_snps
+  end
+
+  def self.stats(mask, triad, gene, genome, reference)
+    specific = []
+    semispecific = []
+    sp_i = 0
+    semi = 0
+    i = 0
+    mask.to_s.each_char do |e|
+      case e
+      when "n","N"
+        i += 1
+      when /[[:lower:]]/ then
+        semispecific << semi
+        semi = 0
+        i += 1
+      when /[[:upper:]]/ then
+        specific     << sp_i
+        semispecific << semi
+        sp_i = 0
+        semi = 0
+        i += 1
+      when "." then
+        semi += 1
+        sp_i += 1
+        i += 1
+      end
+    end
+    {
+      reference: reference,
+      triad: triad,
+      genome: genome,
+      gene: gene,
+      semispecific_mean: semispecific.mean,
+      semispecific_bases: semispecific.size,
+      semispecific_identity: (1 - (semispecific.size.to_f / i)) * 100 ,
+      specific_mean: specific.mean,
+      specific_bases: specific.size,
+      specific_identity: (1 - (specific.size.to_f / i )) * 100,
+      aligned_length: i,
+      specific: specific,
+      semispecific: semispecific
+    }
+  end
+end
+

data/lib/bio/PolyploidTools/NoSNPSequence.rb

@@ -0,0 +1,292 @@
+
+require_relative "SNP"
+require 'bio-samtools-wrapper'
+module Bio::PolyploidTools
+  class SNPSequenceException < RuntimeError 
+  end
+
+  class NoSNPSequence < SNP
+
+    attr_accessor :sequence_original
+    #Format: 
+    #snp name,chromsome from contig,microarray sequence
+    #BS00068396_51,2AS,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
+    def self.parse(reg_str)
+      reg_str.chomp!
+      snp = NoSNPSequence.new
+
+      arr = reg_str.split(",")
+      
+      if arr.size == 3
+        snp.gene, snp.chromosome, snp.sequence_original = reg_str.split(",")
+      elsif arr.size == 2
+       snp.gene, snp.sequence_original = arr
+     else
+       throw SNPSequenceException.new "Need two or three fields to parse, and got #{arr.size} in #{reg_str}"
+      end
+      #snp.position = snp.position.to_i
+      #snp.original.upcase!
+      #snp.snp.upcase!  
+      snp.chromosome. strip!
+      snp.snp_in = snp.chromosome
+      snp.parse_sequence_snp
+      snp.exon_list = Hash.new()
+      snp
+    end
+    
+    def parse_snp
+       
+    end
+
+    def parse_sequence_snp
+       @position = (sequence_original.length / 2).to_i 
+       @original = sequence_original[@position]
+       @snp = @original
+    end
+
+    def to_s
+      "#{gene}:#{chromosome}"
+    end
+
+    def sequences_to_align
+      @sequences_to_align = surrounding_exon_sequences unless @sequences_to_align
+      @sequences_to_align
+    end
+
+     def mask_aligned_chromosomal_snp(chromosome)
+      return nil if  aligned_sequences.values.size == 0
+      names = aligned_sequences.keys
+      parentals =  parental_sequences.keys
+      names = names - parentals
+
+
+      best_target = get_target_sequence(names, chromosome)
+      masked_snps = aligned_sequences[best_target].downcase if aligned_sequences[best_target]
+      masked_snps = "-" * aligned_sequences.values[0].size  unless aligned_sequences[best_target]
+
+      #TODO: Make this chromosome specific, even when we have more than one alignment going to the region we want.
+      i = 0
+      while i < masked_snps.size
+        different = 0
+        cov = 0
+        from_group = 0
+        names.each do | chr |
+          if aligned_sequences[chr] and aligned_sequences[chr][i]  != "-"
+            cov += 1 
+
+            from_group += 1 if chr[0] == chromosome_group
+            #puts "Comparing #{chromosome_group} and #{chr[0]} as chromosomes"
+            if chr != chromosome 
+              $stderr.puts "WARN: No base for #{masked_snps} : ##{i}" unless masked_snps[i].upcase
+              $stderr.puts "WARN: No base for #{aligned_sequences[chr]} : ##{i}" unless masked_snps[i].upcase
+              different += 1  if masked_snps[i].upcase != aligned_sequences[chr][i].upcase 
+            end
+          end
+        end
+        masked_snps[i] = "-" if different == 0
+        masked_snps[i] = "-" if cov == 1
+        masked_snps[i] = "*" if cov == 0
+        expected_snps = names.size - 1
+       #puts "Diferences: #{different} to expected: #{ expected_snps } [#{i}] Genome count (#{from_group} == #{genomes_count})"
+        
+        masked_snps[i] = masked_snps[i].upcase if different == expected_snps and from_group == genomes_count
+
+        i += 1
+      end
+      masked_snps
+    end
+
+    def count_deletions_around(position,target_chromosome)
+      first_aligned = aligned_sequences[target_chromosome]
+
+      pos_start = position - flanking_size
+      pos_end = position + flanking_size
+      pos_start = 0 if pos_start < 0
+      pos_end = first_aligned.size - 1 if pos_end >= first_aligned.size
+      count = 0
+      for i in pos_start..pos_end
+        has_del = false
+
+        aligned_sequences.each_pair do |name, val|  
+          has_del = true if val[i] == '-'
+          #print "#{val[i]}\t"
+        end
+        count += 1 if has_del
+        #print "#{count}\n"
+      end
+      return count
+    end
+
+    def primer_region(target_chromosome, parental_chr )
+      chromosome_seq = aligned_sequences[target_chromosome]
+      names = aligned_sequences.keys
+      target_chromosome = get_target_sequence(names, target_chromosome)
+      chromosome_seq = aligned_sequences[target_chromosome]
+      chromosome_seq = surrounding_exon_sequences[target_chromosome ]if aligned_sequences.size == 0
+      chromosome_seq = "-" * sequence_original.size unless chromosome_seq
+      chromosome_seq = chromosome_seq.downcase
+      #puts chromosome_seq
+      mask = mask_aligned_chromosomal_snp(target_chromosome)
+    
+      pr = PrimerRegion.new
+      pr.homoeologous = false
+      position_in_region = 0
+      parental = chromosome_seq.clone
+      (0..chromosome_seq.size-1).each do |i|
+
+        if chromosome_seq[i] != '-'
+          case   
+          when mask[i] == '-'
+            #When the mask doesnt detect a SNP, so we take the parental
+            parental[i] = chromosome_seq[i] unless Bio::NucleicAcid::is_unambiguous(parental[i])
+          when /[[:upper:]]/.match(mask[i])
+            #This is a good candidate for marking a SNP
+            #We validate that the consensus from the sam file accepts the variation from the chromosomal sequence
+            if parental[i] == '-'
+              parental[i] = mask[i]
+              pr.crhomosome_specific_intron << position_in_region
+            elsif Bio::NucleicAcid.is_valid(parental[i], mask[i])
+              parental[i] = mask[i]
+              pr.chromosome_specific << position_in_region #if count_deletions_around(1,target_chromosome) < 3
+              pr.chromosome_specific_in_mask << i
+            end
+
+          when /[[:lower:]]/.match(mask[i])
+            #this is not that good candidate, but sitll gives specificity
+            if parental[i] == '-'
+              parental[i] = mask[i]
+              pr.almost_crhomosome_specific_intron << position_in_region
+            elsif Bio::NucleicAcid.is_valid(parental[i], mask[i])
+              parental[i] = mask[i].upcase
+              pr.almost_chromosome_specific << position_in_region
+              pr.almost_chromosome_specific_in_mask << i
+            end
+          end #Case closes
+          pr.position_in_mask_from_template[position_in_region] = i
+          position_in_region += 1
+        end #Closes region with bases 
+      end         
+      pr.sequence=parental.gsub('-','')
+      pr
+    end
+
+    def return_primer_3_string(opts={})
+      #puts "return_primer_3_string #{opts.inspect}"
+      left = opts[:left_pos]
+      right = opts[:right_pos]
+      sequence =  opts[:sequence].clone
+      orientation = "forward"
+      if opts[:right_pos]
+        orientation = "forward"
+        if left > right
+          left = sequence.size - left - 1
+          right = sequence.size - right - 1
+          sequence = reverse_complement_string(sequence)
+          orientation = "reverse"
+        end
+        if @variation_free_region > 0
+          check_str = sequence[right+1, @variation_free_region]
+          return nil if check_str != check_str.downcase
+        end
+
+      end
+
+
+      str = "SEQUENCE_ID=#{opts[:name]} #{orientation}\n"
+      str << "SEQUENCE_FORCE_LEFT_END=#{left}\n"
+      str << "SEQUENCE_FORCE_RIGHT_END=#{right}\n" if opts[:right_pos]
+      str << "SEQUENCE_TEMPLATE=#{sequence}\n"
+      str << "=\n"
+
+
+      #In case that we don't have a right primer, we do both orientations
+      unless opts[:right_pos]
+        sequence =  opts[:sequence].clone    
+        left = sequence.size - left - 1
+        orientation = "reverse"
+        sequence = reverse_complement_string(sequence)
+        str << "SEQUENCE_ID=#{opts[:name]} #{orientation}\n"
+        str << "SEQUENCE_FORCE_LEFT_END=#{left}\n"
+        str << "SEQUENCE_TEMPLATE=#{sequence}\n"
+        str << "=\n"
+      end
+
+      str
+    end
+
+    def get_base_in_different_chromosome(position, target_chromosome)
+
+        aligned_sequences.each_pair do |name, val|  
+          next if target_chromosome == name
+          return val[position]
+        end
+    end
+
+    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
+      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
+
+      if pr.homoeologous
+        snp_type = "homoeologous"
+      else
+        snp_type = "non-homoeologous"
+      end
+
+      pr.chromosome_specific.each_with_index do |pos , i|
+        seq_snp =  seq_original.clone
+        #original_base = seq_snp[pos]
+        #puts "___"
+        #puts aligned_sequences.keys.inspect
+        #puts target_chromosome
+        t_chr =  get_target_sequence(aligned_sequences.keys, target_chromosome)
+        other_chromosome_base = get_base_in_different_chromosome(pr.chromosome_specific_in_mask[i], t_chr)
+
+        args = {
+          :name =>"#{gene} A chromosome_specific exon #{snp_type} #{chromosome}", 
+          :left_pos => pos,  
+          :sequence=>seq_snp
+        }
+        
+        seq_snp =  seq_original.clone
+        primer_3_propertes << return_primer_3_string(args)
+        
+        args[:name] = "#{gene} B chromosome_specific exon #{snp_type} #{chromosome}"
+        seq_snp[pos] =  other_chromosome_base.upcase
+        args[:sequence] = seq_snp
+        
+        
+        primer_3_propertes << return_primer_3_string(args)
+      end
+
+  
+      primer_3_propertes
+    end
+
+    def aligned_sequences
+     
+      return @aligned_sequences if @aligned_sequences
+      if sequences_to_align.size <= 1
+        @aligned_sequences = sequences_to_align
+        return @aligned_sequences
+      end
+      options = ['--maxiterate', '1000', '--localpair', '--quiet']
+      mafft = Bio::MAFFT.new( "mafft" , options)
+    #  puts "Before MAFT:#{sequences_to_align.inspect}"
+      report = mafft.query_align(sequences_to_align)
+      @aligned_sequences = report.alignment
+   #   puts "MAFFT: #{report.alignment.inspect}" 
+      @aligned_sequences
+    end
+    
+
+
+   
+
+  end
+end

data/lib/bio/PolyploidTools/PrimerRegion.rb

@@ -0,0 +1,30 @@
+module Bio::PolyploidTools
+  class PrimerRegion
+    attr_accessor :snp_pos, :almost_chromosome_specific_in_mask 
+    attr_accessor :chromosome_specific_in_mask, :sequence 
+    attr_accessor :chromosome_specific, :almost_chromosome_specific
+    attr_accessor :crhomosome_specific_intron , :almost_crhomosome_specific_intron
+    attr_accessor :homoeologous, :position_in_mask_from_template
+
+    def initialize
+
+      @chromosome_specific = Array.new
+      @almost_chromosome_specific = Array.new
+      @crhomosome_specific_intron  = Array.new
+      @almost_crhomosome_specific_intron = Array.new
+      #For deletions
+      @chromosome_specific_in_mask = Array.new
+      @almost_chromosome_specific_in_mask = Array.new
+      @position_in_mask_from_template = Hash.new
+    end
+
+    def tail_candidates
+      @chromosome_specific.size + @almost_chromosome_specific.size
+    end
+
+    def to_fasta
+      ">Primer_#{snp_pos}_#{chromosome_specific.to_s}_#{almost_chromosome_specific.to_s}_#{crhomosome_specific_intron.to_s}_#{almost_crhomosome_specific_intron.to_s}\n#{sequence}\n"
+    end
+
+  end
+end