bio-polyploid-tools 0.9.9 → 0.9.10

checksums.yaml

@@ -1,7 +1,7 @@
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data/VERSION

@@ -1 +1 @@
-0.9.9
+0.9.10

data/bin/marker_to_vcf.rb

@@ -0,0 +1,241 @@
+#!/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[:min_identity] = 90
+options[:filter_best]  = false
+options[:debug]  = false
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: marler_to_vcf.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("-b", "--filter_best", "If set, only keep the best alignment for each chromosome") do 
+    options[:filter_best]  = false
+  end
+
+    opts.on("-D", "--debug", "Validate that the flanking sequences are correct") do 
+    options[:debug]  = true
+  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("-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("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: blast") 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
+
+end.parse!
+options[:database] = options[:path_to_contigs] 
+p options
+p ARGV
+
+
+path_to_contigs=options[:path_to_contigs]
+
+original_name="A"
+snp_in="B"
+
+fasta_reference = nil
+test_file=options[:marker_list]
+
+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)
+#T
+temp_fasta_query="#{output_folder}/to_align.fa"
+temp_contigs="#{output_folder}/contigs_tmp.fa"
+exonerate_file="#{output_folder}/exonerate_tmp.tab"
+vcf_file="#{output_folder}/snp_positions.vcf"
+
+min_identity= options[:min_identity]
+
+@status_file="#{output_folder}/status.txt"
+
+
+def write_status(status)
+  f=File.open(@status_file, "a")
+  f.puts "#{Time.now.to_s},#{status}"
+  f.close
+end
+
+
+snps = Hash.new
+
+fasta_reference_db=nil
+
+#if options[:debug]
+write_status "Loading Reference"
+fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path_to_contigs})
+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 |
+    snp = Bio::PolyploidTools::SNPSequence.parse(line)  
+    snp.genomes_count = options[:genomes_count]
+    snp.snp_in = snp_in
+    snp.original_name = original_name
+    if snp.position 
+      snps[snp.gene] = snp
+    else
+      $stderr.puts "ERROR: #{snp.gene} doesn't contain a SNP"
+    end
+  end
+end
+
+#2. Generate all the fasta files
+write_status "Writing sequences to align"
+written_seqs = Set.new
+file = File.open(temp_fasta_query, "w")
+snps.each_pair do |k,snp|
+  unless written_seqs.include?(snp.gene)
+    written_seqs << snp.gene 
+    file.puts snp.to_fasta
+  end
+end
+file.close
+
+
+#3. Run exonerate on each of the possible chromosomes for the SNP
+#puts chromosome
+#chr_group = chromosome[0]
+write_status "Searching markers in genome"
+exo_f = File.open(exonerate_file, "w")
+contigs_f = File.open(temp_contigs, "w") if options[:extract_found_contigs]
+filename=path_to_contigs 
+#puts filename
+target=filename
+
+fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
+fasta_file.load_fai_entries
+found_contigs = Set.new
+
+def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
+  if aln.identity > min_identity
+    exo_f.puts aln.line
+  end  
+end
+
+Bio::DB::Blast.align({:query=>temp_fasta_query, :target=>options[:database]}) do |aln|
+  do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options)
+end
+
+exo_f.close() 
+
+def print_positions(min_identity:90, filter_best:false, exonerate_filename:"test.exo", snps:{}, reference:nil, out:$stdout) 
+  marker_count=Hash.new { |h, k| h[k] = 1 }
+  File.open(exonerate_filename) do |f|
+    f.each_line do | line |
+      record = Bio::DB::Exonerate::Alignment.parse_custom(line)
+      next unless  record and record.identity >= min_identity
+      snp = snps[record.query_id]                           
+      next unless snp != nil and snp.position.between?( (record.query_start + 1) , record.query_end)
+      begin
+
+        position = record.query_position_on_target(snp.position)
+        q_strand = record.query_strand
+        t_strand = record.target_strand 
+        template = snp.template_sequence
+
+        vulgar = record.exon_on_gene_position(snp.position)
+        tr = vulgar.target_region
+        qr = vulgar.query_region
+        template_pre = template[qr.start - 1 .. snp.position - 1 ]
+        tr.orientation == :forward ? tr.end = position : tr.start = position
+        region = tr
+        target_seq = reference.fetch_sequence(region)
+        target_seq[-1] = target_seq[-1].upcase
+        ref_base = target_seq[-1]
+        ma = ref_base
+        alt_base = [snp.snp, snp.original].join(",")
+
+        if snp.original == ref_base
+          alt_base = snp.snp
+        elsif snp.snp == ref_base
+          alt_base = snp.original
+        end
+
+        if record.target_strand == :reverse
+          alt_base = Bio::Sequence::NA.new(alt_base)
+          ref_base = Bio::Sequence::NA.new(ref_base)
+          alt_base.complement!.upcase!
+          ref_base.complement!.upcase!
+        end
+        
+        info =  ["OR=#{record.target_strand}"]
+        info <<  "SC=#{record.score}"
+        info <<  "PI=#{record.pi}"
+        info <<  "MA=#{ma}"
+        info <<  "TS=#{target_seq}"
+        vcf_line="#{record.target_id}\t#{position}\t#{record.query_id}.path#{marker_count[record.query_id]}\t#{ref_base}\t#{alt_base}\t#{record.pi}\t.\t#{info.join(";")}"
+        #snp2 = Bio::PolyploidTools::SNP.parseVCF( vcf_line )
+        #snp2.setTemplateFromFastaFile(reference)
+        #seq2=snp2.to_polymarker_sequence(50)
+        #info << "PS=#{seq2}"
+        vcf_line="#{record.target_id}\t#{position}\t#{record.query_id}.path#{marker_count[record.query_id]}\t#{ref_base}\t#{alt_base}\t#{record.pi}\t.\t#{info.join(";")}"
+        out.puts(vcf_line)
+        
+        marker_count[record.query_id] += 1
+      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
+
+
+write_status "Printing VCF file"
+#puts snps.inspect
+out = File.open(vcf_file, "w")
+out.puts "##fileformat=VCFv4.2"
+out.puts "##fileDate=#{Time.now.strftime("%Y%m%d")}"
+out.puts "##source=#{$0}"
+out.puts "##reference=file://#{options[:path_to_contigs]}"
+out.puts "##INFO=<ID=OR,Number=1,Type=String,Description=\"Orientation of the alignment of the marker\">"
+out.puts "##INFO=<ID=SC,Number=1,Type=Float,Description=\"Alignment score of the marker\">"
+out.puts "##INFO=<ID=PI,Number=1,Type=Float,Description=\"Percentage of identity of the alignment to the marker\">"
+out.puts "##INFO=<ID=PS,Number=1,Type=String,Description=\"SNP sequence for PolyMarker\">"
+out.puts "##INFO=<ID=MA,Number=1,Type=String,Description=\"Allele based on the original marker sequence\">"
+out.puts "##INFO=<ID=TS,Number=1,Type=String,Description=\"Target sequence before the SNP from the reference\">"
+out.puts "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"
+print_positions(exonerate_filename:exonerate_file, min_identity:95, snps:snps, reference: fasta_reference_db, out:out)
+out.close
+write_status "DONE"
+
+

data/bin/polymarker.rb

@@ -124,7 +124,7 @@ OptionParser.new do |opts|
     options[:scoring] = :het_dels
   end
 
-  opts.on("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: exonerate") do |o|
+  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
@@ -137,7 +137,7 @@ end.parse!
 
 validate_files(options)
 
- options[:database] = options[:path_to_contigs] unless  options[:database] 
+options[:database] = options[:path_to_contigs] unless  options[:database] 
 
 
 if options[:primer_3_preferences][:primer_product_size_range]
@@ -169,7 +169,7 @@ 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)
+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"

data/bin/vcfToPolyMarker.rb

@@ -0,0 +1,82 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+
+require 'csv'
+require 'bio'
+require 'bio-samtools'
+
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+require path
+
+options = {}
+options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection("nrgene");
+
+
+OptionParser.new do |opts|
+	opts.banner = "Usage: polymarker.rb [options]"
+
+	opts.on("-c", "--reference FILE", "File with genome reference to use as database") do |o|
+		options[:path_to_contigs] = o
+	end
+
+	opts.on("-a", "--arm_selection #{Bio::PolyploidTools::ChromosomeArm.getValidFunctions.join('|')}", "Function to decide the chromome arm") do |o|
+		tmp_str = o
+		arr = o.split(",")
+		if arr.size == 2
+			options[:arm_selection] = lambda do |contig_name|
+				separator, field = arr
+				field = field.to_i
+				ret = contig_name.split(separator)[field]
+				return ret
+			end
+		else
+			options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection(o)
+		end
+	end
+
+
+end.parse!
+
+def parseVCFheader(head_line="")
+	##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+
+	m=/##INFO=<ID=(.+),Number=(.+),Type=(.+),Description="(.+)">/.match(head_line)
+	{:id=>m[1],:number=>m[2],:type=>m[3],:desc=>m[4]}
+
+end
+
+
+
+
+header_info = Hash.new
+ref=options[:path_to_contigs]
+
+fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+fasta_reference_db.load_fai_entries 
+
+$stdin.each do |line|  
+
+	h = nil
+	h = parseVCFheader(line) if line.start_with? "##INFO"
+
+	header_info[h[:id]] = h[:desc] if h
+	#puts header_info.inspect
+	next if line.start_with? "##"
+	if line.start_with? "#CHROM"
+		arr = line.split
+		arr = arr.drop(9)
+		arr2 = arr.map { |s| [s.clone().prepend('Cov'), s.clone().prepend('Hap') ]}
+		#header += arr2.join("\t")
+		#puts header
+		next
+	end
+	line.chomp!
+	#puts line
+	snp = Bio::PolyploidTools::SNP.parseVCF( line , options[:arm_selection])
+	#puts snp.inspect
+	snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
+	puts [snp.gene, snp.chromosome ,snp.to_polymarker_sequence(100)].join(",")
+end

data/bio-polyploid-tools.gemspec

@@ -2,19 +2,19 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.9.9 ruby lib
+# stub: bio-polyploid-tools 0.9.10 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.9"
+  s.version = "0.9.10"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
-  s.date = "2018-11-21"
+  s.date = "2019-03-11"
   s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
   s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
-  s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "find_homoeologue_variations.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze]
+  s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "find_homoeologue_variations.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "marker_to_vcf.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze, "vcfToPolyMarker.rb".freeze]
   s.extra_rdoc_files = [
     "README",
     "README.md"
@@ -41,6 +41,7 @@ Gem::Specification.new do |s|
     "bin/mafft_triads.rb",
     "bin/mafft_triads_promoters.rb",
     "bin/map_markers_to_contigs.rb",
+    "bin/marker_to_vcf.rb",
     "bin/markers_in_region.rb",
     "bin/mask_triads.rb",
     "bin/polymarker.rb",
@@ -49,6 +50,7 @@ Gem::Specification.new do |s|
     "bin/snps_between_bams.rb",
     "bin/tag_stats.rb",
     "bin/vcfLineToTable.rb",
+    "bin/vcfToPolyMarker.rb",
     "bio-polyploid-tools.gemspec",
     "conf/defaults.rb",
     "conf/primer3_config/dangle.dh",
@@ -183,7 +185,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.7.7".freeze
+  s.rubygems_version = "2.6.14".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then

data/lib/bio/PolyploidTools/Mask.rb

@@ -1,3 +1,5 @@
+require 'bio'
+
 class Array
   def sum
     inject(0.0) { |result, el| result + el }
@@ -9,7 +11,6 @@ class Array
 end
 
 module Bio::PolyploidTools::Mask
-
   def self.find_end(seqs)
     size = seqs.values[0].size
     names = seqs.keys
@@ -112,3 +113,4 @@ module Bio::PolyploidTools::Mask
     }
   end
 end
+

data/lib/bio/PolyploidTools/SNP.rb

@@ -1,11 +1,12 @@
 require 'bio'
 module Bio::PolyploidTools
   class SNPException < RuntimeError 
-   end
+  end
+  
   class SNP
-
     #GENE,ORIGINAL,POS,SNP
     attr_accessor :gene, :original, :position, :snp, :snp_in, :original_name
+    attr_accessor :contig
     attr_accessor :exon_list
     attr_accessor :container
     attr_accessor :flanking_size, :ideal_min, :ideal_max
@@ -20,6 +21,7 @@ module Bio::PolyploidTools
     attr_accessor :repetitive
     attr_accessor :hit_count
     attr_accessor :snp_type
+    attr_accessor :orientation
 
     #Format: 
     #Gene_name,Original,SNP_Pos,pos,chromosome
@@ -35,28 +37,57 @@ module Bio::PolyploidTools
       snp.snp.upcase!
       snp.snp.strip!  
       snp.chromosome.strip!
-   
+      
       snp.use_reference = false
       snp
     end
 
-    def setTemplateFromFastaFile(fastaFile ,flanking_size = 100)
+    #Format:
+    #IWGSC_CSS_1AL_scaff_1455974  127 test_snp    C  T  135.03 .  
+    def self.parseVCF(vcf_line, chr_arm_parser: Bio::PolyploidTools::ChromosomeArm.getArmSelection("first_two") )
+      snp = SNP.new
+      arr = vcf_line.split("\t")
+      snp.gene     = arr[2]
+      snp.original = arr[3]
+      snp.position = arr[1]
+      snp.snp = arr[4] 
+      snp.chromosome = chr_arm_parser.call(arr[0]) 
+      snp.contig = arr[0]
+      snp.position.strip!
+      snp.position =  snp.position.to_i
+      snp.original.upcase!
+      snp.original.strip!
+      snp.snp.upcase!
+      snp.snp.strip!  
+      snp.chromosome.strip! 
+      snp.orientation = :forward
+
+      info = arr[7]
+      if info
+        details =  info.scan(/(\w+)=([\w|.]+)/).collect { |id, value| { :id => id, :value => value }}
+        details.each do |e|   
+          snp.orientation = :reverse if e[:id] == "OR" and e[:value] == "reverse"
+        end
+      end
+      return snp
+    end
+
+    def setTemplateFromFastaFile(fastaFile ,flanking_size: 100)
       reg = Bio::DB::Fasta::Region.new
       reg.entry = gene
       reg.entry = @contig if @contig
-      #puts reg.entry 
-      #puts @contig
-      #puts gene
       reg.start = position - flanking_size
-      reg.end = position + flanking_size +1
+      reg.end = position + flanking_size + 1
       reg.orientation = :forward
-      entry = fastaFile.index.region_for_entry(gene)
+      entry = fastaFile.index.region_for_entry(reg.entry)
       reg.start = 1 if reg.start < 1
       reg.end = entry.length if reg.end > entry.length
       amb = Bio::NucleicAcid.to_IUAPC("#{original}#{snp}")
       @position = @position - reg.start + 1
       @position = 1 if @position < 1
+      #puts "about to fetch"
       self.template_sequence = fastaFile.fetch_sequence(reg)
+      #puts "done fetching"
       template_sequence[position - 1] = amb
     end
 
@@ -83,15 +114,24 @@ module Bio::PolyploidTools
 
     def to_polymarker_sequence(flanking_size, total:nil)
       out = template_sequence.clone
-      #puts "changing: #{position} #{flanking_size} len: #{total}"
-      out[position-1]  = "[#{original}/#{snp}]"
+      snp_seq = "[#{original}/#{snp}]"
+      p = position-1 
+      if orientation == :reverse
+        p = out.length - p - 1
+        s = Bio::Sequence::NA.new(out)
+        s1 = Bio::Sequence::NA.new(original)
+        s2 = Bio::Sequence::NA.new(snp) 
+        out = s.reverse_complement
+        snp_seq = "[#{s1.reverse_complement}/#{s2.reverse_complement}]"
+
+      end
+
+      out[p]  = snp_seq
       start = position - flanking_size - 1
-      #puts "Start: #{start}"
       start = 0 if start < 0
       total = flanking_size * 2 unless total
       total += 5
-      #puts "Total: #{total}"
-      out[start , total ]
+      out[start , total ].upcase
     end
     
     def snp_id_in_seq
@@ -187,7 +227,7 @@ module Bio::PolyploidTools
       self.position - self.covered_region.start
     end
 
-    def padded_position (pos)
+    def padded_position(pos)
       pos + left_padding
     end
 

data/lib/bio/PolyploidTools/SNPSequence.rb

@@ -18,9 +18,10 @@ module Bio::PolyploidTools
       arr = reg_str.split(",")
       
       if arr.size == 3
-        snp.gene, snp.chromosome, snp.sequence_original = reg_str.split(",")
+        snp.gene, snp.chromosome, snp.sequence_original = arr
       elsif arr.size == 2
        snp.gene, snp.sequence_original = arr
+       snp.chromosome = ""
      else
        throw SNPSequenceException.new "Need two or three fields to parse, and got #{arr.size} in #{reg_str}"
       end
@@ -51,4 +52,4 @@ module Bio::PolyploidTools
    
 
   end
-end
+end

data/lib/bio/db/blast.rb

@@ -79,7 +79,7 @@ module Bio::DB::Blast
 	def self.align(opts={})
 		target=opts[:target]
 		query=opts[:query]
-		max_target_seqs = 15
+		max_target_seqs = 6 #TODO: Actually add this as an argument to PolyMarker. 
 		max_target_seqs = opts[:max_hits] * 2 if opts[:max_hits]
 		cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
 

data/lib/bio/db/exonerate.rb

@@ -190,6 +190,26 @@ module Bio::DB::Exonerate
       nil
     end
 
+    def query_position_on_target(position, base:0)
+      vulgar = exon_on_gene_position(position)
+      qr = vulgar.query_region
+      tr = vulgar.target_region
+      
+      offset = qr.orientation == :forward ? position - qr.start + 1 : qr.end - position
+
+      #puts vulgar.to_s
+      #puts "SNP position: #{position}"
+      #puts vulgar.query_region
+      #puts vulgar.query_region.orientation
+      #puts "Offset query: #{offset}"
+      #puts vulgar.target_region
+      #puts vulgar.target_region.orientation
+
+      new_pos = tr.orientation == :forward ? offset + tr.start - 1 :  tr.end - offset + 1
+
+      return new_pos
+    end
+
     def tarpostion_from_query_position(position)
       ret = nil
       vulgar_block = exon_on_gene_position(position)
@@ -206,7 +226,6 @@ module Bio::DB::Exonerate
     end
   end
 
-
   class Vulgar
     attr_reader :label, :query_length, :target_length, :query_start, :query_end, :target_start, :target_end, :record, :snp_in_gap
     def initialize(label, ql, tl, target_start, target_multiply, query_start, query_multiply, record)

data/lib/bio/db/primer3.rb

@@ -552,7 +552,18 @@ module Bio::DB::Primer3
     #CL3339Contig1:T509C AvocetS chromosome_specific exon 4D forward 
     def parse_header
       #puts "Parsing header: '#{self.sequence_id}'"
-      @snp, @line, @type, @in, @polymorphism, @chromosome, @orientation   = self.sequence_id.split(" ")  
+      arr = self.sequence_id.split(" ")
+
+      #if arr.size == 7 This validation can be useful to get the best primers regardless of the chromosome, 
+      #But it is commented as it will require further testing. 
+      @snp, @line, @type, @in, @polymorphism, @chromosome, @orientation  = arr  
+      #else 
+      #  if arr.size == 6
+      #    @snp, @line, @type, @in, @polymorphism, @orientation  = arr
+      #    @chromosome = ""   
+      #  end 
+      #end
+
       @type = @type.to_sym
       if @in
         @in = @in.to_sym == :exon 

data/lib/bioruby-polyploid-tools.rb

@@ -9,7 +9,9 @@ require 'json'
 #require 'bio/db/fasta'
 
 #puts "Loading all... #{Dir[File.dirname(__FILE__) + "/bio/*/*.rb"]}"
+module Bio::PolyploidTools
 
+end
 Dir[File.dirname(__FILE__) + "/bio/*.rb"].each {|file| 
  # puts file 
   require_relative file }
@@ -22,4 +24,5 @@ require_relative File.dirname(__FILE__) + "/../conf/defaults.rb"
 
 
 #require_relative "bio/BFRTools.rb"
-#require_relative "bio/PolyploidTools/ExonContainer.rb"
+#require_relative "bio/PolyploidTools/ExonContainer.rb"
+

data/test/test_snp_parsing.rb

@@ -36,17 +36,50 @@ class TestSNPparsing < Test::Unit::TestCase
     assert_equal(snp.contig, "IWGSC_CSS_1AL_scaff_1455974")
     assert_equal(snp.chromosome, "1A", "The chromosome wasnt parsed: #{snp.chromosome}")
     assert_equal(snp.position, 127, "The position is not parsed: #{snp.position}")
-    #snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = 100)
+    #snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
     region = fasta_reference_db.index.region_for_entry(snp.contig).get_full_region
     snp.full_sequence = fasta_reference_db.fetch_sequence(region)
 
-    assert_equal(snp.template_sequence, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag")
-    assert_equal(snp.sequence_original, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag")
+    assert_equal(snp.template_sequence, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase)
+    assert_equal(snp.sequence_original, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase)
     assert_equal(snp.position, 101)
     assert_equal(snp.original, "C")
     assert_equal(snp.snp, "T")
+  end
+
+  def test_vcf_line
+    ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
     
-    
+    fasta_reference_db.load_fai_entries 
+    vcf="IWGSC_CSS_1AL_scaff_1455974	127	test_snp	C	T	135.03	.	"
+
+    chr_arm_parser = Bio::PolyploidTools::ChromosomeArm.getArmSelection("embl");
+    snp = Bio::PolyploidTools::SNP.parseVCF(vcf, chr_arm_parser: chr_arm_parser)
+    assert_equal(snp.gene , "test_snp", "The original name was not parsed: #{snp.gene}")
+    assert_equal("1A", snp.chromosome, "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(127, snp.position, "The position is not parsed: #{snp.position}")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size:  100)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga",     snp.template_sequence)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase, snp.to_polymarker_sequence(100))
+    assert_equal(101,snp.position)
+    assert_equal("C",snp.original)
+    assert_equal("T",snp.snp)
+
+    vcf="IWGSC_CSS_1AL_scaff_1455974\t127\ttest_snp\tC\tT\t135.03\t.\tOR=reverse"
+
+    chr_arm_parser = Bio::PolyploidTools::ChromosomeArm.getArmSelection("embl");
+    snp = Bio::PolyploidTools::SNP.parseVCF(vcf, chr_arm_parser: chr_arm_parser)
+    assert_equal(snp.gene , "test_snp", "The original name was not parsed: #{snp.gene}")
+    assert_equal("1A", snp.chromosome, "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(127, snp.position, "The position is not parsed: #{snp.position}")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size:  100)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga",     snp.template_sequence)
+    assert_equal("TCTTGTACCTACCGAGTGCAGCATGCTACGTACCTTATAGCCAGAAGCCTTGACGTGGTGGATGCGGTCTCCAAAGCGCTTGTCAAGTCCGGGTACGACAA[G/A]GAGACCTGTAAGCAGCGCGTGCTCATACAGTCAGAGGACGCCCCGGTGCTTGCGGCGTTCAAGACGTTCCCCAAGTTCCAGCGGGTGCTGACGATCGAG", snp.to_polymarker_sequence(100))
+    assert_equal(101,snp.position)
+    assert_equal("C",snp.original)
+    assert_equal("T",snp.snp)
+
   end
 
   def test_reference_snp
@@ -60,9 +93,9 @@ class TestSNPparsing < Test::Unit::TestCase
     assert_equal(snp.gene , "IWGSC_CSS_1AL_scaff_1455974", "The original name was not parsed: #{snp.gene}")
     assert_equal("1A", snp.chromosome, "The chromosome wasnt parsed: #{snp.chromosome}")
     assert_equal(127, snp.position, "The position is not parsed: #{snp.position}")
-    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = 100)
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
     assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga",     snp.template_sequence)
-    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag", snp.to_polymarker_sequence(100))
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase, snp.to_polymarker_sequence(100))
     assert_equal(101,snp.position)
     assert_equal("C",snp.original)
     assert_equal("T",snp.snp)
@@ -70,14 +103,14 @@ class TestSNPparsing < Test::Unit::TestCase
     flanking_size = 3
 
     snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1DL_scaff_2258883,A,12498,C,1D")
-    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = flanking_size)
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: flanking_size)
     assert_equal(4,snp.position)
     assert_equal("A",snp.original)
     assert_equal("C",snp.snp)
     assert_equal("gatM", snp.template_sequence)
 
     snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1BL_scaff_3810460,G,1,T,1B")
-    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size = flanking_size)
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: flanking_size)
     assert_equal(1,snp.position)
     assert_equal("G",snp.original)
     assert_equal("T",snp.snp)
@@ -85,4 +118,4 @@ class TestSNPparsing < Test::Unit::TestCase
   end
 
   
-end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.9.9
+  version: 0.9.10
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-21 00:00:00.000000000 Z
+date: 2019-03-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -127,6 +127,7 @@ executables:
 - mafft_triads.rb
 - mafft_triads_promoters.rb
 - map_markers_to_contigs.rb
+- marker_to_vcf.rb
 - markers_in_region.rb
 - mask_triads.rb
 - polymarker.rb
@@ -135,6 +136,7 @@ executables:
 - snps_between_bams.rb
 - tag_stats.rb
 - vcfLineToTable.rb
+- vcfToPolyMarker.rb
 extensions: []
 extra_rdoc_files:
 - README
@@ -161,6 +163,7 @@ files:
 - bin/mafft_triads.rb
 - bin/mafft_triads_promoters.rb
 - bin/map_markers_to_contigs.rb
+- bin/marker_to_vcf.rb
 - bin/markers_in_region.rb
 - bin/mask_triads.rb
 - bin/polymarker.rb
@@ -169,6 +172,7 @@ files:
 - bin/snps_between_bams.rb
 - bin/tag_stats.rb
 - bin/vcfLineToTable.rb
+- bin/vcfToPolyMarker.rb
 - bio-polyploid-tools.gemspec
 - conf/defaults.rb
 - conf/primer3_config/dangle.dh
@@ -320,7 +324,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology