bio-polymarker 1.3.2

data/bin/polymarker.rb

@@ -0,0 +1,410 @@
+#!/usr/bin/env ruby
+require 'bio'
+require 'rubygems'
+require 'pathname'
+require 'bio-samtools-wrapper'
+require 'optparse'
+require 'set'
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')
+require path
+
+
+
+def validate_files(o)
+  [
+    o[:path_to_contigs], 
+    o[:marker_list], 
+    o[:snp_list], 
+    o[:mutant_list],
+    o[:reference]
+  ].flatten.compact.each do |f|  
+        raise IOError.new "Unable to read #{f}" unless File.exist? f
+    end
+end 
+
+options = {}
+options[:path_to_contigs] = "/tgac/references/external/projects/iwgsc/css/IWGSC_CSS_all_scaff_v1.fa"
+options[:chunks] = 1
+options[:bucket_size] = 0
+options[:bucket] = 1
+options[:model] = "est2genome"
+options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection("nrgene");
+options[:flanking_size] = 150;
+options[:variation_free_region] = 0 
+options[:extract_found_contigs] = false
+options[:genomes_count] = 3
+options[:min_identity] = 90
+options[:scoring] = :genome_specific
+options[:database]  = false
+options[:filter_best]  = false
+options[:aligner] = :blast
+options[:max_hits] = 8
+options[:max_specific_primers]  = 20
+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]"
+
+  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
+  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
+  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
+  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|
+    options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection(o)
+   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("-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
+
+  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
+
+  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
+
+  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: #{options[:aligner]}") do |o|
+    raise "Invalid aligner" unless o == "exonerate" or o == "blast" 
+    options[:aligner] = o.to_sym
+  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
+  end
+
+  opts.on("-H", "--max_hits INT", "Maximum number of hits to the reference. If there are more hits than this value, the marker is ignored") do |o|
+    options[:max_hits] = o.to_i
+  end
+
+  opts.on("-S", "--max_specific_primers INT", "Maximum number of candidate primers to attempt to design. Default: #{options[:max_specific_primers]} ") do |o|
+    options[:max_specific_primers]  = o.to_i
+  end
+  
+end.parse!
+
+
+validate_files(options)
+
+options[:database] = options[:path_to_contigs] unless  options[:database] 
+
+
+if options[:primer_3_preferences][:primer_product_size_range]
+  range = options[:primer_3_preferences][:primer_product_size_range]
+  range_arr = range.split("-")
+  min = range_arr[0].to_i
+  max = range_arr[1].to_i
+  raise  Bio::DB::Exonerate::ExonerateException.new "Range #{range} is invalid!" unless max > min
+  options[:flanking_size] = max
+end
+
+#p options
+#p ARGV
+
+
+#TODO: Use temporary files somewhere in the file system and add traps to delete them/forward them as a result. 
+#TODO: Make all this parameters
+
+path_to_contigs=options[:path_to_contigs]
+
+original_name="A"
+snp_in="B"
+
+fasta_reference = nil
+#test_file="/Users/ramirezr/Dropbox/JIC/PrimersToTest/test_primers_nick_and_james_1.csv"
+test_file=options[:marker_list]  if options[:marker_list]
+test_file=options[:snp_list] if options[:snp_list]
+test_file=options[:mutant_list] if options[:mutant_list]
+fasta_reference = options[:reference]
+output_folder="#{test_file}_primer_design_#{Time.now.strftime('%Y%m%d-%H%M%S')}" 
+output_folder= options[:output_folder] if  options[:output_folder]
+Dir.mkdir(output_folder) unless Dir.exist?(output_folder)
+#TODO Make this tmp files
+temp_fasta_query="#{output_folder}/to_align.fa"
+temp_contigs="#{output_folder}/contigs_tmp.fa"
+exonerate_file="#{output_folder}/exonerate_tmp.tab"
+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"
+min_identity= options[:min_identity]
+
+@status_file="#{output_folder}/status.txt"
+
+primer_3_config=File.expand_path(File.dirname(__FILE__) + '/../conf/primer3_config')
+model=options[:model] 
+
+def write_status(status)
+  f=File.open(@status_file, "a")
+  f.puts "#{Time.now.to_s},#{status}"
+  f.close
+end
+
+Signal.trap("ABRT")  do
+  write_status "ERROR: Job aborted. Please try a small number of primers." 
+  Signal.trap("SIGABRT", "DEFAULT") # restore handler
+  Process.kill("ABRT", 0)   
+end
+
+Signal.trap("TERM")  do 
+  write_status "ERROR: Job terminated. Please try a small number of primers." 
+  Signal.trap("SIGTERM", "DEFAULT") # restore handler
+  exit
+end
+
+snps = Array.new
+
+begin
+  
+write_status "Loading Reference"
+#0. Load the fasta index 
+fasta_reference_db = nil
+if fasta_reference
+  fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>fasta_reference})
+  fasta_reference_db.load_fai_entries
+  write_status "Fasta reference: #{fasta_reference}"
+end
+
+#1. Read all the SNP files 
+#chromosome = nil
+write_status "Reading SNPs"
+File.open(test_file) do | f |
+  f.each_line do | line |
+    # p line.chomp!
+    snp = nil
+    if options[:marker_list] #List with Sequence
+      snp = Bio::PolyploidTools::SNPSequence.parse(line)  
+    elsif options[:snp_list] and options[:reference] #List and fasta file
+      snp = Bio::PolyploidTools::SNP.parse(line)
+      entry = fasta_reference_db.index.region_for_entry(snp.gene)
+      if entry
+       region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
+       snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+     else
+      write_status "WARN: Unable to find entry for #{snp.gene}"
+    end
+    elsif options[:mutant_list] and options[:reference] #List and fasta file
+      snp = Bio::PolyploidTools::SNPMutant.parse(line)
+      entry = fasta_reference_db.index.region_for_entry(snp.contig)
+      if entry
+       region = fasta_reference_db.index.region_for_entry(snp.contig).get_full_region
+       snp.full_sequence = fasta_reference_db.fetch_sequence(region)
+     else
+      write_status "WARN: Unable to find entry for #{snp.gene}"
+    end
+  else
+    raise Bio::DB::Exonerate::ExonerateException.new "Wrong number of arguments. " 
+  end
+  raise Bio::DB::Exonerate::ExonerateException.new "No SNP for line '#{line}'" if snp == nil
+  snp.max_hits = options[:max_hits]
+  snp.genomes_count = options[:genomes_count]
+  snp.snp_in = snp_in
+  snp.original_name = original_name
+  if snp.position 
+    snps << snp
+  else
+    $stderr.puts "ERROR: #{snp.gene} doesn't contain a SNP"
+  end
+  end
+end
+
+#1.1 Close fasta file
+#fasta_reference_db.close() if fasta_reference_db
+#2. Generate all the fasta files
+write_status "Writing sequences to align"
+written_seqs = Set.new
+file = File.open(temp_fasta_query, "w")
+snps.each do |snp|
+  unless written_seqs.include?(snp.gene)
+    written_seqs << snp.gene 
+    file.puts snp.to_fasta
+  end
+end
+file.close
+
+#3. Run exonerate on each of the possible chromosomes for the SNP
+#puts chromosome
+#chr_group = chromosome[0]
+write_status "Searching markers in genome"
+exo_f = File.open(exonerate_file, "w")
+contigs_f = nil
+contigs_f = File.open(temp_contigs, "w") if options[:extract_found_contigs]
+filename=path_to_contigs 
+#puts filename
+target=filename
+
+fasta_file = Bio::DB::Fasta::FastaFile.new(fasta: target)
+fasta_file.load_fai_entries
+
+found_contigs = Set.new
+
+
+def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options, contigs_f: nil)
+  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
+      if options[:extract_found_contigs]
+        region = entry.get_full_region
+        seq = fasta_file.fetch_sequence(region)
+        contigs_f.puts(">#{aln.target_id}\n#{seq}") 
+      end
+    end
+  end  
+
+end
+
+Bio::DB::Blast.align({:query=>temp_fasta_query, :target=>options[:database], :model=>model, :max_hits=>options[:max_hits]}) do |aln|
+  do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options, contigs_f: contigs_f)
+end if options[:aligner] == :blast
+
+Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model}) do |aln|
+  do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options, contigs_f: contigs_f)
+end if options[:aligner] == :exonerate
+ 
+exo_f.close() 
+
+
+ 
+exo_f.close() 
+contigs_f.close() if options[:extract_found_contigs]
+
+#4. Load all the results from exonerate and get the input filename for primer3
+#Custom arm selection function that only uses the first two characters. Maybe
+#we want to make it a bit more cleaver
+write_status "Reading best alignment on each chromosome"
+
+
+container= Bio::PolyploidTools::ExonContainer.new
+container.flanking_size=options[:flanking_size] 
+container.gene_models(temp_fasta_query)
+container.chromosomes(target)
+container.add_parental({:name=>snp_in})
+container.add_parental({:name=>original_name})
+container.max_hits = options[:max_hits]
+snps.each do |snp|
+  snp.container = container
+  snp.flanking_size = container.flanking_size
+  snp.variation_free_region = options[:variation_free_region]
+  container.add_snp(snp)
+end
+container.add_alignments({
+  :exonerate_file=>exonerate_file, 
+  :arm_selection=>options[:arm_selection], 
+  :min_identity=>min_identity,
+  :filter_best=>options[:filter_best]})
+
+
+#4.1 generating primer3 file
+write_status "Finding genome-specific positions"
+file = File.open(exons_filename, "w")
+container.print_fasta_snp_exones(file)
+file.close
+write_status "Running primer3"
+
+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,  max_specific_primers: options[:max_specific_primers] )
+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
+write_status "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
+
+snps.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,repetitive,total_hits"
+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())}
+
+write_status "DONE"
+rescue StandardError => e
+  write_status "ERROR\t#{e.message}"
+  raise e 
+rescue Exception => e
+  write_status "ERROR\t#{e.message}"
+  raise e  
+end