bio-polymarker 1.3.2

data/conf/primer3_config/tstack_tm_inf.ds

@@ -0,0 +1,256 @@
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data/lib/bio/BFRTools.rb

@@ -0,0 +1,465 @@
+require 'rubygems'
+#require 'extensions/all'
+#require 'bio-samtools'
+#require 'bio/db/pileup'
+#require 'bio/db/vcf'
+require 'pathname'
+#require_relative 'BIOExtensions.rb'
+
+
+require 'bio'
+require 'bio-samtools-wrapper'
+
+require "set"
+require 'systemu'
+require 'json'
+#require 'strmask'
+
+
+module Bio::BFRTools
+  
+  
+  
+  class BFRToolsException < StandardError; end
+
+
+  class Container
+
+    attr_reader :putative_snps, :processed_regions, :total_length, :parental_1_sam,  :parental_2_sam,  :bulk_1_sam,  :bulk_2_sam
+    attr_reader :parental_1_name, :parental_2_name, :bulk_1_name, :bulk_2_name, :reference_db
+
+    BASES = [:A, :C, :G, :T]
+    #Sets the reference file
+    def reference(path)
+      @reference_db = Bio::DB::Fasta::FastaFile.new(fasta: path)
+      @reference_path = path
+    end
+
+    def reference_sequence(region)
+      @reference_db.fetch_sequence(region)
+    end
+
+    #Sets the sorted BAM file of the first parental
+    #It accepts the following arguments
+    #:name=>A name for thie parental 1 (optional). If not provided, 
+    #:path=>
+    def parental_1(opts)
+      raise BFRToolsException.new("Missing path for parental 1") if opts[:path] == nil
+      path = Pathname.new(opts[:path])
+      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_path = path
+
+    end 
+
+    #Sets the sorted BAM file of the second parental
+    def parental_2(opts)
+      raise BFRToolsException.new("Missing path for parental 2") if opts[:path] == nil
+      path = Pathname.new(opts[:path])
+      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_path = path
+    end
+
+    #Sets the sorted BAM file of the first bulk
+    def bulk_1(opts)
+      raise BFRToolsException.new("Missing path for bulk 1") if opts[:path] == nil
+      path = Pathname.new(opts[:path])
+      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_path = path
+    end 
+
+    #Sets the sorted BAM file of the second bulk
+    def bulk_2(opts)
+      raise BFRToolsException.new("Missing path for bulk 2") if opts[:path] == nil
+      path = Pathname.new(opts[:path])
+      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_path = path
+    end     
+
+
+    def self.snps_between(seq1, seq2)
+      snps=0
+      for i in (0..seq1.size)
+        snps += 1 if seq1[i] != seq2[i]
+      end
+      snps
+    end
+  end
+
+  class BFRLine
+    attr_reader :original_base, :variation_base, :position, :bulk_1_ratio, :bulk_2_ratio, :bfr
+
+
+  end
+
+  class BFRRegion < Bio::DB::Fasta::Region
+    BASES = [:A, :C, :G, :T]
+    attr_reader :parental_1_sequence, :parental_2_sequence, :bulk_1_sequence, :bulk_2_sequence, :snp_count
+    attr_reader :ratios_bulk_1, :ratios_bulk_2, :avg_cov_bulk_1, :avg_cov_bulk_2, :coverages_1, :coverages_2, :bases_bulk_1, :bases_bulk_2
+
+    def initialize(opts)
+      opts = { :min_cov=>20, :max_snp_1kbp => 5 }.merge!(opts)
+      reg = Bio::DB::Fasta::Region.parse_region(opts[:region])
+      self.entry = reg.entry
+      self.start = reg.start
+      self.end   = reg.end
+      @BFRs = nil
+      opts[:region] = reg
+      @container = opts[:container]
+
+      parental_1_reg = @container.parental_1_sam.fetch_region(opts)
+      parental_2_reg = @container.parental_2_sam.fetch_region(opts)
+      bulk_1_reg = @container.bulk_1_sam.fetch_region(opts)
+      bulk_2_reg = @container.bulk_2_sam.fetch_region(opts)
+      
+    
+
+      @parental_1_sequence = parental_1_reg.consensus
+      @parental_2_sequence = parental_2_reg.consensus
+      
+      @bulk_1_sequence = bulk_1_reg.consensus
+      @bulk_2_sequence = bulk_2_reg.consensus
+
+      @snp_count = Container.snps_between( @parental_1_sequence , @parental_2_sequence )
+
+      @ratios_bulk_1 = bulk_1_reg.base_ratios
+      @ratios_bulk_2 = bulk_2_reg.base_ratios
+
+      @bases_bulk_1 = bulk_1_reg.bases
+      @bases_bulk_2 = bulk_2_reg.bases
+
+      @avg_cov_bulk_1 = bulk_1_reg.average_coverage
+      @avg_cov_bulk_2 = bulk_2_reg.average_coverage
+
+      @coverages_1 =  bulk_1_reg.coverages
+      @coverages_2 =  bulk_2_reg.coverages
+
+    end
+
+    def get_bfr_lines(opts = {})
+     
+      opts = { :min_cov=>20, :max_snp_1kbp => 5 }.merge!(opts)
+      p opts.inspect
+      region = self
+      line  = String.new
+      info = Array.new
+      
+      for i in (0..region.size-1)
+        
+        if region.coverages_1[i] > opts[:min_cov] and region.coverages_2[i] > opts[:min_cov]
+          BASES.each do |base|
+
+            info.clear
+            if  Bio::NucleicAcid.is_valid( region.parental_1_sequence[i],  base.to_s  ) and 
+              not  Bio::NucleicAcid.is_valid( region.parental_2_sequence[i],  base.to_s  )
+              info << :first
+            end
+
+            if   Bio::NucleicAcid.is_valid( region.parental_2_sequence[i],  base.to_s  ) and 
+              not Bio::NucleicAcid.is_valid( region.parental_1_sequence[i],  base.to_s  )
+              info << :second
+            end
+
+
+            for informative in info
+              l = region.get_bfr_line(i, base, informative)
+              puts l << "\n"
+              line << l << "\n"
+
+              #     output.print  line , "\n"
+            end
+          end
+        end
+      end
+      line
+    end
+
+
+    def snp_1kbp
+      @snp_count.to_f * 1000 / self.size.to_f
+    end
+
+    def bfrs
+      return @BFRs if @BFRs
+      @BFRs = Hash.new
+      
+      [:first, :second].each do | reference |
+        @BFRs[reference] = Hash.new
+        BASES.each do |base|
+          @BFRs[reference][base] = Array.new
+        end
+      end
+      
+
+      for i in (0..self.size-1)
+        ratios_1 = @ratios_bulk_1[i]
+        ratios_2 = @ratios_bulk_2[i]
+        BASES.each do |base|
+          
+          if ratios_1[base] == 0 and ratios_2[base] == 0
+            bfr1 = 0
+            bfr2  = 0
+          elsif ratios_1[base] == 0
+           bfr1  = 0
+           bfr2 = Float::INFINITY
+          elsif ratios_2[base] == 0
+           bfr1 = Float::INFINITY
+            bfr2 = 0
+            #bfr = Float::INFINITY
+          else
+            bfr1  =  ratios_1[base] / ratios_2[base]
+            bfr2 =  ratios_2[base] / ratios_1[base]
+          end
+          @BFRs[:first][base] << bfr1
+          @BFRs[:second][base] << bfr2
+        end
+      end
+      @BFRs
+    end
+
+    def get_bfr_line(position, base, reference)
+      if(reference == :first)
+        informative = @container.parental_1_name
+        ref_base = @parental_2_sequence[position]
+      elsif(reference == :second )
+        informative = @container.parental_2_name
+        ref_base = @parental_1_sequence[position]
+      else
+        raise BFRToolsException.new ("The reference for the line should be :first or :second, but was " + reference.to_s )
+      end
+      
+      relative_position = self.start +  position 
+      
+      bfr = bfrs[reference][base][position]
+      cov_1 = @coverages_1[position]
+      cov_2 = @coverages_2[position]
+      ratios_1 = @ratios_bulk_1[position][base]
+      ratios_2 = @ratios_bulk_2[position][base]
+      base_1_count = @bases_bulk_1[position][base.to_sym]
+      base_2_count = @bases_bulk_2[position][base.to_sym]
+      #puts "bases_1 #{@bases_bulk_1[position].to_s}"
+      #puts "bases_2 #{@bases_bulk_2[position].to_s}"
+      line = String.new
+      line << @container.parental_1_name  << "\t" << @container.parental_2_name << "\t" <<  @container.bulk_1_name << "\t" << @container.bulk_2_name << "\t" << self.entry << "\t"
+      line << ref_base  << "\t" << relative_position.to_s 
+      line << "\t" << base.to_s << "\t" 
+      line << bfr.round(2).to_s << "\t"  
+      line << cov_1.to_s << "\t" << cov_2.to_s  << "\t" 
+      line << informative 
+      line << "\t" << ratios_1.round(2).to_s << "\t" << ratios_2.round(2).to_s
+      line << "\t" << base_1_count.to_s << "\t" << base_2_count.to_s
+      line
+    end
+
+    def to_multi_fasta
+      fasta_string = String.new
+      fasta_string << ">"<< self.to_s << ":" << @container.parental_1_name << "\n" << @parental_1_sequence << "\n"
+      fasta_string << ">"<< self.to_s << ":" << @container.parental_2_name << "\n" << @parental_2_sequence << "\n"
+      fasta_string << ">"<< self.to_s << ":" << @container.bulk_1_name << "\n" << @bulk_1_sequence << "\n"
+      fasta_string << ">"<< self.to_s << ":" << @container.bulk_2_name << "\n" << @bulk_2_sequence << "\n"
+      fasta_string 
+    end
+
+    def to_json (opts)
+      #      puts JSON.dump self
+      #      JSON.dump self
+      #{}"{\"firstName\": \"John\"}"
+      out = String.new
+      out << "{" 
+      out << "\"Parental_1\" : \"" << @container.parental_1_name << "\"\n"
+      out << "\"Parental 2\" : \"" << @container.parental_2_name << "\"\n"
+      out << "\"Bulk 1\" :  \"" <<  @container.bulk_1_name << "\"\n"
+      out << "\"Bulk 2\" : \"" << @container.bulk_2_name << "\"\n"
+      out << "\"Positions\" : " << (1..self.size).to_a.to_json << "\n" #TODO: Make this for any subsection, so we can subquery in case we are working on something bigger
+      out << "\"Parental_1_consensus\":" << @parental_1_sequence .split(//).to_json << "\n"
+      out << "\"Parental_2_consensus\":" << @parental_2_sequence .split(//).to_json << "\n"
+      out << "\"Bulk_1_consensus\":" << @bulk_1_sequence .split(//).to_json << "\n"
+      out << "\"Bulk_1_coverage\":" << @coverages_1.to_json << "\n"
+      #  puts BASES
+      
+      BASES.each do |base|
+        out << "\"Bases_Bulk_1"  << base.to_s << "\":" <<  base_count_for_base(base, @bases_bulk_1).join(",") << "\n"
+        out << "\"Ratios_Bulk_1" << base.to_s << "\":" << base_ratios_for_base(base, @ratios_bulk_1).join(",")  << "\n"
+      end
+      out << "\"Bulk_2_consensus\":" << @bulk_2_sequence .split(//).join(",") << "\n"
+      out << "\"Bulk_2_coverage\":" << @coverages_2.join(",") << "\n"
+
+      BASES.each do |base|
+        out << "\"Bases_Bulk_2"<< base.to_s << "\":" <<  base_count_for_base(base, @bases_bulk_2).join(",") << "\n"
+        out << "\"Ratios_Bulk_2" << base.to_s << "\":" << base_ratios_for_base(base, @ratios_bulk_2).join(",")  << "\n"
+      end
+      BASES.each do |base|
+        out << "\"BFR" << base.to_s << "\":"  << bfrs[:first][base].join(",") << "\n"
+      end
+      #     << "\t" << @container.bulk_2_name << "\t" << self.entry << "\t"
+      out << "}"
+      out
+
+    end
+
+    def to_csv
+      out = String.new
+      out << "Parental 1," << @container.parental_1_name << "\n"
+      out << "Parental 2," << @container.parental_2_name << "\n"
+      out << "Bulk 1, " <<  @container.bulk_1_name << "\n"
+      out << "Bulk 2," << @container.bulk_2_name << "\n"
+      out << "Positions," << (1..self.size).to_a.join(",") << "\n"
+      out << "Parental 1 consensus," << @parental_1_sequence .split(//).join(",") << "\n"
+      out << "Parental 2 consensus," << @parental_2_sequence .split(//).join(",") << "\n"
+      out << "Bulk 1 consensus," << @bulk_1_sequence .split(//).join(",") << "\n"
+      out << "Bulk 1 coverage," << @coverages_1.join(",") << "\n"
+      #  puts BASES
+      BASES.each do |base|
+        out << "Bases Bulk 1"<< base.to_s << "," <<  base_count_for_base(base, @bases_bulk_1).join(",") << "\n"
+        out << "Ratios Bulk 1 " << base.to_s << "," << base_ratios_for_base(base, @ratios_bulk_1).join(",")  << "\n"
+      end
+      out << "Bulk 2 consensus," << @bulk_2_sequence .split(//).join(",") << "\n"
+      out << "Bulk 2 coverage," << @coverages_2.join(",") << "\n"
+
+      BASES.each do |base|
+        out << "Bases Bulk 2   "<< base.to_s << "," <<  base_count_for_base(base, @bases_bulk_2).join(",") << "\n"
+        out << "Ratios Bulk 2 " << base.to_s << "," << base_ratios_for_base(base, @ratios_bulk_2).join(",")  << "\n"
+      end
+      BASES.each do |base|
+        out << "BFRs" << base.to_s << ","  << bfrs[:first][base].join(",") << "\n"
+      end
+      #     << "\t" << @container.bulk_2_name << "\t" << self.entry << "\t"
+      out
+    end
+
+    def base_ratios_for_base(base, ratios_matrix)
+      ratios = Array.new
+      for i in (0..ratios_matrix.size-1)
+        ratios << ratios_matrix[i][base]
+      end
+      ratios
+    end
+
+    def base_count_for_base(base, base_matrix)
+      bases = Array.new
+      for i in (0..base_matrix.size-1)
+        bases << base_matrix[i][base]
+      end
+      bases
+    end
+
+  end
+
+
+  class BFRContainer < Container
+
+    def init_counters
+      @putative_snps      = 0
+      @proccesed_regions  = 0
+      @not_enogh_coverage = 0
+      @total_avg_coverage_bulk_1 = 0.0
+      @total_avg_coverage_bulk_2 = 0.0
+      @total_snp_1kbp = 0.0
+      @no_snps = 0
+      @too_many_snps = 0
+
+    end
+    def print_header(opts={}) 
+      output = opts[:output_file_stats] ? opts[:output_file_stats] : $stderr
+      output.print "#bulk_1\tbulk_2\tProcessed_regions\tputative_snps\tno_snps\ttoo_many_snps\tno_enough_coverage\tavg_cov_bulk_1\tavg_cov_bulk_2\tavg_snp_1kbp\n"
+    end
+
+    def print_stats(opts={}) 
+      output = opts[:output_file_stats] ? opts[:output_file_stats] : $stderr
+      output.print @bulk_1_name, "\t", @bulk_2_name, "\t"
+      output.print @proccesed_regions, "\t", @putative_snps, "\t", @no_snps, "\t", @too_many_snps,"\t", @not_enogh_coverage, "\t"
+      output.print @total_avg_coverage_bulk_1/@proccesed_regions, "\t",@total_avg_coverage_bulk_2/@proccesed_regions, "\t" 
+      output.print @total_snp_1kbp / @proccesed_regions,"\n"
+    end
+
+    def get_region(opts={})
+      opts[:container] = self
+      region = BFRRegion.new(opts)
+    end
+
+    def process_region(opts={})        
+      opts = { :min_cov=>20, :max_snp_1kbp => 10, :max_per=>0.20 }.merge!(opts)
+
+      @proccesed_regions += 1
+      output = opts[:output_file] ? opts[:output_file] : $stdout
+      print_output = opts[:output_file] ? true : false
+      opts[:container] = self
+
+      region = BFRRegion.new(opts)
+
+      #puts region.to_multi_fasta
+
+      @total_snp_1kbp += region.snp_1kbp 
+     # puts "SNPS: #{region.snp_1kbp}"
+      if region.snp_count == 0
+        @no_snps += 1 
+        print_output = false 
+      end
+
+      if region.snp_1kbp  > opts[:max_snp_1kbp]
+        @too_many_snps += 1
+        print_output = false
+      end
+
+
+
+      @total_avg_coverage_bulk_2 += region.avg_cov_bulk_2
+      @total_avg_coverage_bulk_1 += region.avg_cov_bulk_1
+
+      if region.avg_cov_bulk_2 < opts[:min_cov] or region.avg_cov_bulk_1 < opts[:min_cov]
+        @not_enogh_coverage += 1
+        print_output = false
+      end
+
+      info = Array.new
+
+      if print_output
+        for i in (0..region.size-1)
+          if region.coverages_1[i] > opts[:min_cov] and region.coverages_2[i] > opts[:min_cov]
+            BASES.each do |base|
+
+              info.clear
+              if  Bio::NucleicAcid.is_valid( region.parental_1_sequence[i],  base.to_s  ) and 
+                not  Bio::NucleicAcid.is_valid( region.parental_2_sequence[i],  base.to_s  )
+                info << :first
+              end
+
+              if   Bio::NucleicAcid.is_valid( region.parental_2_sequence[i],  base.to_s  ) and 
+                not Bio::NucleicAcid.is_valid( region.parental_1_sequence[i],  base.to_s  )
+                info << :second
+              end
+
+
+              for informative in info
+                line = region.get_bfr_line(i, base, informative)
+                output.print  line , "\n"
+              end
+            end
+          end
+        end
+      end
+
+
+      @parental_1_sam.mpileup_clear_cache region
+      @parental_2_sam.mpileup_clear_cache region
+      @bulk_2_sam.mpileup_clear_cache region
+      @bulk_1_sam.mpileup_clear_cache region
+      return region
+    end
+
+  end
+
+
+end
+