bio-polyploid-tools 0.1.0

data/bin/homokaryot_primers.rb

@@ -0,0 +1,155 @@
+#!/usr/bin/env ruby
+require 'bio'
+require 'rubygems'
+require 'pathname'
+require 'bio-samtools'
+
+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
+
+
+#@snp_map=Hash.new
+
+class HomokaryotContainer < Bio::PolyploidTools::ExonContainer
+  
+  
+  def add_snp_file(filename, chromosome, snp_in, original_name)
+    flanking_size = 100
+     File.open(filename) do | f |
+       f.each_line do | line |
+         snp = Bio::PolyploidTools::SNP.parse(line)
+         snp.flanking_size = flanking_size
+         if snp.position > 0
+           snp.container = self
+           snp.chromosome = chromosome
+           snp.snp_in = snp_in
+           snp.original_name = original_name
+           snp.use_reference = true
+           snp.container = self
+           @snp_map[snp.gene] = Array.new unless   @snp_map[snp.gene] 
+           @snp_map[snp.gene] << snp   
+         end
+       end
+     end
+     
+     
+  end
+  
+  def print_primer_3_exons (file, target_chromosome , parental )
+    @snp_map.each do | gene, snp_array|
+      snp_array.each do |snp|
+        string = snp.primer_3_string( snp.chromosome, parental )
+        file.puts string if string.size > 0
+
+      end 
+    end
+  end
+end
+
+class Bio::PolyploidTools::SNP
+  
+  @aligned = false
+  
+  def aligned_snp_position
+     return local_position
+     
+  end
+  
+  def aligned_sequences
+      
+    @aligned_sequences = parental_sequences    
+    @aligned_sequences["A"][local_position] = original
+    @aligned_sequences["B"][local_position] = snp
+    return @aligned_sequences
+  end
+end
+
+
+
+
+
+snp_file = ARGV[0]
+reference_file = ARGV[1]
+
+snp_in="A"
+original_name="B"
+snps = Array.new
+
+#0. Load the fasta index 
+fasta_reference_db = nil
+if reference_file
+  fasta_reference_db = Bio::DB::Fasta::FastaFile.new(reference_file)
+  fasta_reference_db.load_fai_entries
+  p "Fasta reference: #{reference_file}"
+end
+#1. Read all the SNP files 
+#All the SNPs should be on the same chromosome as the first SNP. 
+chromosome = nil
+File.open(snp_file) do | f |
+  f.each_line do | line |
+    # p line.chomp!
+    snp = nil
+    if ARGV.size == 1 #List with Sequence
+      snp = Bio::PolyploidTools::SNPSequence.parse(line)  
+    elsif ARGV.size == 2 #List and fasta file
+      snp = Bio::PolyploidTools::SNP.parse(line)
+      region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
+      snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+    else
+      rise Bio::DB::Exonerate::ExonerateException.new "Wrong number of arguments. " 
+    end
+    rise Bio::DB::Exonerate::ExonerateException.new "No SNP for line '#{line}'" if snp == nil
+    snp.snp_in = snp_in
+    snp.original_name = original_name
+    snps << snp
+    chromosome = snp.chromosome unless chromosome
+    raise Bio::DB::Exonerate::ExonerateException.new "All the snps should come from the same chromosome" if chromosome != snp.chromosome
+  end
+end
+
+
+container = HomokaryotContainer.new
+container.add_parental({:name=>snp_in})
+container.add_parental({:name=>original_name})
+container.gene_models(reference_file)
+
+output_folder="#{snp_file}_primer_design_#{Time.now.strftime('%Y%m%d-%H%M%S')}/"
+Dir.mkdir(output_folder)
+primer_3_input="#{output_folder}primer_3_input_temp"
+primer_3_output="#{output_folder}primer_3_output_temp"
+container.add_snp_file(snp_file, "PST130",  snp_in, original_name)
+primer_3_config=File.expand_path(File.dirname(__FILE__) + '/../conf/primer3_config')
+output_primers="#{output_folder}primers.csv"
+
+file = File.open(primer_3_input, "w")
+file.puts("PRIMER_PRODUCT_SIZE_RANGE=50-150")
+file.puts("PRIMER_MAX_SIZE=25")
+file.puts("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1")
+file.puts("PRIMER_LIBERAL_BASE=1")
+file.puts("PRIMER_NUM_RETURN=5")
+file.puts("PRIMER_THERMODYNAMIC_PARAMETERS_PATH=#{primer_3_config}/")
+
+
+container.print_primer_3_exons(file, "PST130",snp_in)
+
+file.close
+
+
+Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output})
+
+#2. Pick the best primer and make the primer3 output
+kasp_container=Bio::DB::Primer3::KASPContainer.new
+kasp_container.line_1=original_name
+kasp_container.line_2=snp_in
+
+snps.each do |snp|
+  kasp_container.add_snp(snp) 
+end
+
+kasp_container.add_primers_file(primer_3_output)
+header = "Marker,SNP,RegionSize,SNP_type,#{snp_in},#{original_name},common,primer_type,orientation,#{snp_in}_TM,#{original_name}_TM,common_TM,selected_from,product_size"
+File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }

data/bin/map_markers_to_contigs.rb

@@ -0,0 +1,66 @@
+#!/usr/bin/env ruby
+require 'bio'
+require 'optparse'
+
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << 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
+
+markers = nil
+
+options = {}
+OptionParser.new do |opts|
+  
+  opts.banner = "Usage: polymarker.rb [options]"
+
+  opts.on("-c", "--chromosome CHR", "chromosome (1A, 3B, etc)") do |o|
+    options[:chromosome] = o.upcase
+  end
+  opts.on("-r", "--reference FASTA", "reference with the contigs") do |o|
+    options[:reference] = o
+  end
+  opts.on("-m", "--map CSV", "File with the map and sequence \n Header: INDEX_90K,SNP_ID,SNP_NAME,CHR,COORDINATES_CHR,MAP_ORDER,CHR_ARM,DISTANCE_CM,SEQUENCE") do |o|
+    options[:map] = o
+  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
+
+map = Bio::PolyploidTools::ArmMap.new
+map.chromosome = options[:chromosome]
+map.global_reference(reference)
+log "Reading markers file"
+Bio::PolyploidTools::Marker.parse(options[:map]) do |marker|
+ if options[:chromosome] == marker.chr
+    map.markers[marker.snp_name] = marker 
+  end
+end
+
+
+
+fasta_tmp="markers_#{options[:chromosome]}.fa"
+contigs_tmp="contigs_#{options[:chromosome]}.fa"
+aln_tmp="align_#{options[:chromosome]}.psl"
+contigs_map="contigs_map_#{options[:chromosome]}.fa"
+map_with_contigs="contigs_map_#{options[:chromosome]}.csv"
+
+#1. Prints the sequences to print according to the chromosome to search
+log "Writing markers: #{fasta_tmp}"
+map.print_fasta_markers(fasta_tmp)
+log "Writing contigs: #{contigs_tmp}"
+map.print_fasta_contigs_from_reference(contigs_tmp)
+log "Aligning markers #{aln_tmp}" 
+map.align_markers(aln_tmp)
+log "printing contigs with markers #{contigs_map}"
+map.print_fasta_contigs_for_markers(contigs_map)
+log "printing map with contigs #{map_with_contigs}"
+map.print_map_with_contigs(map_with_contigs)

data/bin/markers_in_region.rb

@@ -0,0 +1,42 @@
+#!/usr/bin/env ruby
+
+#This uses the map output from map_markers_to_contigs.rb 
+#You need a reference with the name of the contigs, containing the chromosome 
+#arm and a list of sequences to map. The algorithm creates a smaller reference 
+#file, so the search only spans across the contigs in the region. This should
+#allow to use a refined mapping algorithm. 
+require 'bio'
+require 'optparse'
+
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << 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
+
+markers = nil
+
+options = {}
+OptionParser.new do |opts|
+  
+  opts.banner = "Usage: polymarker.rb [options]"
+
+  opts.on("-c", "--chromosome CHR", "chromosome (1A, 3B, etc)") do |o|
+    options[:chromosome] = o.upcase
+  end
+  opts.on("-r", "--reference FASTA", "reference with the contigs") do |o|
+    options[:reference] = o
+  end
+  opts.on("-m", "--map CSV", "File with the map and sequence \n Header: INDEX_90K,SNP_ID,SNP_NAME,CHR,COORDINATES_CHR,MAP_ORDER,CHR_ARM,DISTANCE_CM,SEQUENCE") do |o|
+    options[:map] = o
+  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

data/bin/polymarker.rb

@@ -0,0 +1,219 @@
+#!/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
+
+
+
+
+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"
+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("-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("-r", "--reference FILE", "Fasta file with the sequence for the markers (to complement --snp_list)") do |o|
+    options[:reference] = o
+  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
+  
+    
+end.parse!
+
+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]
+
+snp_in="A"
+original_name="B"
+fasta_reference = nil
+#test_file="/Users/ramirezr/Dropbox/JIC/PrimersToTest/test_primers_nick_and_james_1.csv"
+test_file=options[:marker_list]
+test_file=options[:snp_list] if options[:snp_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)
+#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"
+
+primer_3_config=File.expand_path(File.dirname(__FILE__) + '/../conf/primer3_config')
+model=options[:model] 
+
+
+min_identity= 90
+snps = Array.new
+
+#0. Load the fasta index 
+fasta_reference_db = nil
+if fasta_reference
+  fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta_reference)
+  fasta_reference_db.load_fai_entries
+  p "Fasta reference: #{fasta_reference}"
+end
+
+
+#1. Read all the SNP files 
+#All the SNPs should be on the same chromosome as the first SNP. 
+#chromosome = nil
+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)
+      region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
+      snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+    else
+      rise Bio::DB::Exonerate::ExonerateException.new "Wrong number of arguments. " 
+    end
+    rise Bio::DB::Exonerate::ExonerateException.new "No SNP for line '#{line}'" if snp == nil
+    snp.snp_in = snp_in
+    snp.original_name = original_name
+    snps << snp
+#    chromosome = snp.chromosome unless chromosome
+  #  raise Bio::DB::Exonerate::ExonerateException.new "All the snps should come from the same chromosome" if chromosome != snp.chromosome
+  end
+end
+
+#1.1 Close fasta file
+#fasta_reference_db.close() if fasta_reference_db
+#2. Generate all the fasta files
+
+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]
+exo_f = File.open(exonerate_file, "w")
+contigs_f = File.open(temp_contigs, "w")
+filename=path_to_contigs 
+puts filename
+target=filename
+
+fasta_file = Bio::DB::Fasta::FastaFile.new(target)
+fasta_file.load_fai_entries
+
+found_cointigs = Set.new
+Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model}) do |aln|
+  if aln.identity > min_identity
+    exo_f.puts aln.line
+    unless found_cointigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file. 
+      found_cointigs.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}")
+    end
+  end  
+end
+ 
+exo_f.close()
+contigs_f.close()
+
+#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
+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
+arm_selection_embl = lambda do | contig_name|
+  ret = contig_name.split('_')[2][0,2]
+  return ret
+end
+
+container= Bio::PolyploidTools::ExonContainer.new
+container.flanking_size=100
+container.gene_models(temp_fasta_query)
+container.chromosomes(temp_contigs)
+container.add_parental({:name=>snp_in})
+container.add_parental({:name=>original_name})
+snps.each do |snp|
+  snp.container = container
+  snp.flanking_size = container.flanking_size
+  container.add_snp(snp)
+end
+container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>arm_selection_embl, :min_identity=>min_identity})
+
+file = File.open(exons_filename, "w")
+container.print_fasta_snp_exones(file)
+file.close
+
+file = File.open(primer_3_input, "w")
+file.puts("PRIMER_PRODUCT_SIZE_RANGE=50-150")
+file.puts("PRIMER_MAX_SIZE=25")
+file.puts("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1")
+file.puts("PRIMER_LIBERAL_BASE=1")
+file.puts("PRIMER_NUM_RETURN=5")
+file.puts("PRIMER_THERMODYNAMIC_PARAMETERS_PATH=#{primer_3_config}/")
+container.print_primer_3_exons(file, nil, snp_in)
+file.close
+
+Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output})
+
+#5. Pick the best primer and make the primer3 output
+kasp_container=Bio::DB::Primer3::KASPContainer.new
+kasp_container.line_1=snp_in
+kasp_container.line_2=original_name
+
+snps.each do |snp|
+  kasp_container.add_snp(snp) 
+end
+
+kasp_container.add_primers_file(primer_3_output)
+header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{snp_in},#{original_name},common,primer_type,orientation,#{snp_in}_TM,#{original_name}_TM,common_TM,selected_from,product_size"
+File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
+