bio-polyploid-tools 0.7.3 → 0.8.0

data/bin/find_homoeologue_variations.rb

@@ -0,0 +1,385 @@
+#!/usr/bin/env ruby
+require 'bio'
+require 'rubygems'
+require 'pathname'
+require 'bio-samtools'
+require 'optparse'
+require 'set'
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << 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
+
+
+class Bio::PolyploidTools::ExonContainer
+   def add_alignments(opts=Hash.new) 
+      opts = { :min_identity=>90 }.merge!(opts)
+      exonerate_filename = opts[:exonerate_file]
+      arm_selection = opts[:arm_selection]
+
+      unless arm_selection
+        arm_selection = lambda do | contig_name |
+          ret = contig_name[0,3]       
+          return ret
+        end
+      end
+
+      File.open(exonerate_filename) do |f|
+        f.each_line do | line |
+          record = Bio::DB::Exonerate::Alignment.parse_custom(line)
+          if  record and record.identity >= opts[:min_identity]
+            snp_array = @snp_map[record.query_id]
+            if snp_array != nil
+              snp_array.each do |snp|                            
+                if snp != nil and snp.position.between?( (record.query_start + 1) , record.query_end)
+                  begin
+                    exon = record.exon_on_gene_position(snp.position)
+                    snp.add_exon(exon, arm_selection.call(record.target_id))
+                  rescue Bio::DB::Exonerate::ExonerateException
+                    $stderr.puts "Failed for the range #{record.query_start}-#{record.query_end} for position #{snp.position}"
+                  end
+                end
+              end
+            end
+          end
+        end
+      end
+    end
+end
+
+class Bio::DB::Primer3::SNP
+
+  def to_s
+     "#{gene}:#{snp_from.chromosome}"
+  end
+
+end
+class Bio::DB::Primer3::Primer3Record
+
+
+  def best_pair
+    return @best_pair if @best_pair
+    @best_pair = nil
+    @total_caps = 100
+    @primerPairs.each do | primer |
+      capital_count = "#{primer.left.sequence}#{primer.right.sequence}".scan(/[A-Z]/).length
+      if @best_pair.nil?
+        @best_pair = primer 
+        @total_caps = capital_count
+        next
+      end
+      if capital_count < @total_caps
+        @best_pair = primer 
+        @total_caps = capital_count
+      end
+      if primer.size < @best_pair.size 
+        @best_pair = primer 
+        @total_caps = capital_count
+      end
+    end
+    #@best_pair = @primerPairs.min
+    @best_pair
+  end
+
+#CL3339Contig1:T509C AvocetS chromosome_specific exon 4D forward 
+  def parse_header
+    @snp, @line, @type, @in, @polymorphism, @chromosome, @orientation   = self.sequence_id.split(" ")  
+    @type = @type.to_sym
+    if @in
+      @in = @in.to_sym == :exon 
+    else
+      @exon = false
+    end
+
+    if @polymorphism.to_sym == :homoeologous
+      @homoeologous = true
+    else
+      @homoeologous = false
+    end
+    @parsed = true
+    @orientation = @orientation.to_sym
+  end
+
+  def score
+    best_pair
+#    puts "score"
+ #   puts self.inspect
+    ret = 0
+    ret += @scores[type]
+    ret += @scores[:exon] if exon?
+    ret -= @total_caps * 10  
+    ret -= product_length
+    ret
+  end
+
+  def to_s
+      "#{gene}:#{snp_from.chromosome}"
+  end
+
+   def left_primer_snp(snp)
+      tmp_primer = String.new(left_primer)
+      #if self.orientation == :forward
+      #  base_original = snp.original 
+      #  base_snp = snp.snp
+      #elsif self.orientation == :reverse
+      #  base_original = reverse_complement_string(snp.original )
+      #  base_snp = reverse_complement_string(snp.snp)
+      #else
+      #  raise Primer3Exception.new "#{self.orientation} is not a valid orientation"
+      #end
+
+      # puts "#{snp.to_s} #{self.orientation} #{tmp_primer[-1] } #{base_original} #{base_snp}"
+      #if tmp_primer[-1] == base_original
+      #  tmp_primer[-1] = base_snp
+      #elsif tmp_primer[-1] == base_snp
+      #  tmp_primer[-1] = base_original  
+      #else
+      #  raise Primer3Exception.new "#{tmp_primer} doesnt end in a base in the SNP #{snp.to_s}"
+      #end
+      #puts "tmp_primer: #{tmp_primer}"
+      return tmp_primer
+    end
+
+end
+
+arm_selection_functions = Hash.new;
+
+
+arm_selection_functions[:arm_selection_first_two] = lambda do | contig_name |
+  ret = contig_name[0,2]       
+  return ret
+end
+
+#Function to parse stuff like: "IWGSC_CSS_1AL_scaff_110"
+#Or the first two characters in the contig name, to deal with 
+#pseudomolecules that start with headers like: "1A"
+#And with the cases when 3B is named with the prefix: v443
+arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
+  
+  arr = contig_name.split('_')
+  ret = "U"
+  ret = arr[2][0,2] if arr.size >= 3
+  ret = "3B" if arr.size == 2 and arr[0] == "v443"
+  ret = arr[0][0,2] if arr.size == 1   
+  return ret
+end
+
+arm_selection_functions[:arm_selection_morex] = lambda do | contig_name |
+  ret = contig_name.split(':')[0].split("_")[1];       
+  return ret
+end
+
+arm_selection_functions[:scaffold] = lambda do | contig_name |
+  ret = contig_name;       
+  return ret
+end
+
+markers = nil
+
+options = {}
+options[:model] = "est2genome"
+options[:min_identity] = 90
+options[:extract_found_contigs] = false
+options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
+options[:genomes_count] = 3
+
+
+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: find_homoeologue_variations.rb [options]"
+
+  opts.on("-c", "--sequences FASTA", "Sequence of the region to searc") do |o|
+    options[:sequences] = o
+  end
+  opts.on("-r", "--reference FASTA", "reference with the contigs") do |o|
+    options[:reference] = o
+  end
+  opts.on("-o", "--output DIR", "Directory to write the output") do |o|
+    options[:output] = 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("-x", "--extract_found_contigs", "If present, save in a separate file the contigs with matches. Useful to debug.") do |o|
+    options[:extract_found_contigs] = true
+  end
+  
+end.parse!
+#reference="/Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa"
+reference = options[:reference] if options[:reference]
+throw raise Exception.new(), "Reference has to be provided" unless reference
+sequences = options[:sequences] if options[:sequences]
+throw raise Exception.new(), "Fasta file with sequences has to be provided" unless sequences
+output_folder = options[:output] if options[:output]
+throw raise Exception.new(), "An output directory has to be provided" unless output_folder
+model=options[:model] 
+Dir.mkdir(output_folder)
+min_identity= options[:min_identity]
+
+exonerate_file="#{output_folder}/exonerate_tmp.tab"
+temp_contigs="#{output_folder}/contigs_tmp.fa"
+primer_3_input="#{output_folder}/primer_3_input_temp"
+primer_3_output="#{output_folder}/primer_3_output_temp"
+exons_filename="#{output_folder}/exons_genes_and_contigs.fa"
+output_primers="#{output_folder}/primers.csv"
+output_to_order="#{output_folder}/primers_to_order.csv"
+
+fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>reference})
+fasta_file.load_fai_entries
+
+original_name="A"
+snp_in="B"
+
+ arm_selection = options[:arm_selection]
+
+unless arm_selection
+   arm_selection = lambda do | contig_name |
+      ret = contig_name[0,3]       
+      return ret
+    end
+end
+begin
+log "Reading exons"
+exons = Array.new
+Bio::FlatFile.auto(sequences) do |ff|
+  ff.each do |entry|
+    fields = Array.new
+    fields << entry.definition
+    fields << arm_selection.call(entry.definition)
+    fields << entry.seq
+    
+    line = fields.join(",")
+    snp =  Bio::PolyploidTools::NoSNPSequence.parse(line)
+    snp.genomes_count = options[:genomes_count]
+    exons << snp
+     
+  end
+end
+
+
+
+log "Searching markers in genome"
+found_contigs = Set.new
+exo_f = File.open(exonerate_file, "w")
+contigs_f = File.open(temp_contigs, "w") if options[:extract_found_contigs]
+Bio::DB::Exonerate.align({:query=>sequences, :target=>reference, :model=>model}) do |aln|
+	if aln.identity > min_identity
+    exo_f.puts aln.line
+    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
+      seq = fasta_file.fetch_sequence(region)
+      contigs_f.puts(">#{aln.target_id}\n#{seq}") if options[:extract_found_contigs]
+    end
+  end  
+end
+exo_f.close() 
+contigs_f.close() if options[:extract_found_contigs]
+
+
+
+log "Reading best alignment on each chromosome"
+
+container= Bio::PolyploidTools::ExonContainer.new
+container.flanking_size=options[:flanking_size] 
+container.gene_models(sequences)
+container.chromosomes(temp_contigs)
+container.add_parental({:name=>"A"})
+container.add_parental({:name=>"B"})
+exons.each do |exon|
+  exon.container = container
+  exon.flanking_size = 50
+  exon.variation_free_region = options[:variation_free_region]
+#  puts exon.inspect
+  container.add_snp(exon)
+
+end
+container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>options[:arm_selection] , :min_identity=>min_identity})
+
+#4.1 generating primer3 file
+log "Running primer3"
+file = File.open(exons_filename, "w")
+container.print_fasta_snp_exones(file)
+file.close
+
+file = File.open(primer_3_input, "w")
+
+Bio::DB::Primer3.prepare_input_file(file, options[:primer_3_preferences])
+added_exons = container.print_primer_3_exons(file, nil, snp_in)
+file.close
+
+Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output}) if added_exons > 0
+
+#5. Pick the best primer and make the primer3 output
+log "Selecting best primers"
+kasp_container=Bio::DB::Primer3::KASPContainer.new
+kasp_container.line_1= original_name
+kasp_container.line_2= snp_in
+
+if options[:scoring] == :het_dels
+  kasp_container.scores = Hash.new
+  kasp_container.scores[:chromosome_specific] = 0
+  kasp_container.scores[:chromosome_semispecific] = 1000
+  kasp_container.scores[:chromosome_nonspecific] = 100    
+end
+
+exons.each do |snp|
+  snpk = kasp_container.add_snp(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"
+File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
+
+kasp_container.snp_hash.each_pair do |name, kaspSNP|  
+  #puts kaspSNP.snp_from.surrounding_exon_sequences.inspect
+  #puts kaspSNP.first_product
+  #puts kaspSNP.realigned_primers
+
+  out_fasta_products = "#{output_folder}/#{name}.fa"
+  File.open(out_fasta_products, 'w') { |f| f.write(kaspSNP.realigned_primers_fasta) }
+
+
+end
+
+File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails()) }
+
+log "DONE"
+rescue StandardError => e
+  log "ERROR\t#{e.message}"
+  $stderr.puts e.backtrace
+  raise e 
+rescue Exception => e
+  log "ERROR\t#{e.message}"
+  $stderr.puts e.backtrace
+  raise e  
+end
+#puts container.inspect 
+
+#container.snp_map.each do | gene, snp_array|
+#  snp_array.each do |e|
+ #   puts e.inspect
+#    puts e.aligned_sequences_fasta
+#  end
+#end
+

data/bin/get_longest_hsp_blastx_triads.rb

@@ -0,0 +1,66 @@
+#!/usr/bin/env ruby
+require 'optparse'
+require 'bio'
+require 'csv'
+#$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+#$: << File.expand_path('.')
+#path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polyploid-tools.rb')
+#require path
+
+options = {}
+options[:identity] = 50
+options[:min_bases] = 200
+options[:blastx] = "-"
+
+OptionParser.new do |opts|
+  
+  opts.banner = "Usage: filter_blat.rb [options]"
+
+  opts.on("-p", "--blastx FILE", "BLAST XML  file") do |o|
+    options[:blastx] = o
+  end
+  opts.on("-i", "--identity FLOAT", "Minimum percentage identity") do |o|
+    options[:identity] = o.to_f
+  end
+  opts.on("-c", "--min_bases int", "Minimum alignment length (default 200)") do |o|
+    options[:min_bases] = o.to_i
+  end
+
+  opts.on("-t", "--triads FILE", "CSV file with the gene triad names in the named columns 'A','B' and 'D' ") do |o|
+    options[:triads] = o
+  end
+  
+end.parse!
+
+valid_pairs_A_B = Hash.new
+valid_pairs_A_D = Hash.new
+valid_pairs_B_D = Hash.new
+
+CSV.foreach(options[:triads], headers:true ) do |row|
+  valid_pairs_A_B[row['A']] = row['B']
+  valid_pairs_A_D[row['A']] = row['D']
+  valid_pairs_B_D[row['B']] = row['D']
+end
+
+stream = ARGF
+stream = IO.open(options[:blastx]) unless  options[:blastx] == "-"
+puts "Loaded #{valid_pairs_B_D.length} triads"
+$stdout.flush
+
+blast_report = Bio::FlatFile.new(Bio::Blast::Report, stream)
+
+blast_report.each_entry do |report| 
+  puts "Hits for " + report.query_def + " against " + report.db
+  $stdout.flush
+  report.each do |hit|
+    query  = hit.query_id.split("-")[0]
+    target = hit.target_id.split("-")[0]
+    if valid_pairs_A_B[query] == target or valid_pairs_A_D[query] == target or valid_pairs_B_D[query] == target  
+      puts hit.target_id, "\t", hit.evalue, "\n" if hit.evalue < 0.001
+      puts hit.inspect
+    end
+    
+  end
+end
+
+stream.close unless  options[:blat_file] == "-"