bio-polyploid-tools 0.6.1 → 0.7.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 9c92adc72342ddf7d7d51e28fc7ec8fd5c9cec96
+  metadata.gz: 330ed2e80e9d4bc4146e88f1705633cde7554dc6
+  data.tar.gz: 123b1efc4cb49358be17f1913ed68af241b8232b
 SHA512:
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-  data.tar.gz: 94753063d0ad792a47d5b2f4b5e09fe6f88c3e8a66516127afb069bb51dec05b12f50f0e0223e2f84d49e97a5e84c5eb66d2c57736b6657a094378e0b0daaea4
+  metadata.gz: f5eec1a30cdb7365d1bccae60e0c5b89b4939dbae7b928d0d30d1bc88b4b2f193b710894120d756f252c2b76d93b7c3bcf700e9b729973f15481325978fcf049
+  data.tar.gz: e84c2c06bd35049fd90c7b4a8a7a475a59030e757ee0a7506c68ab9aa4419818c3ddc389a820f9de35b4c839d81b8efd3a25c3ff284f8e4d8940ca11b8de71c9

data/VERSION

@@ -1 +1 @@
-0.6.1
+0.7.0

data/bin/filter_blat_by_target_coverage.rb

@@ -43,7 +43,7 @@ options[:identity] = 95
 options[:covered] = 60
 OptionParser.new do |opts|
   
-  opts.banner = "Usage: polymarker.rb [options]"
+  opts.banner = "Usage: filter_blat_by_target_coverage.rb [options]"
 
   opts.on("-p", "--psl FILE", "PSL file") do |o|
     options[:blat_file] = o.upcase

data/bin/filter_exonerate_by_identity.rb

@@ -0,0 +1,38 @@
+#!/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
+
+options = {}
+options[:identity] = 95
+options[:covered] = 90
+OptionParser.new do |opts|
+  
+  opts.banner = "Usage: filter_exonerate_by_identity.rb [options]"
+
+  opts.on("-e", "--exo FILE", "Exonerate alignment produced by polymarker or with the following ryo: 'RESULT:\\t%S\\t%pi\\t%ql\\t%tl\\t%g\\t%V\\n'") do |o|
+    options[:exo_file] = o.upcase
+  end
+  opts.on("-i", "--identity FLOAT", "Minimum percentage identity") do |o|
+    options[:identity] = o.to_f
+  end
+  opts.on("-c", "--covered FLOAT", "Minimum percentage coverage") do |o|
+    options[:covered] = o.to_f
+  end
+  
+end.parse!
+
+
+exo_file = options[:exo_file]
+min_identity = options[:identity];
+min_coverage = options[:covered]
+File.foreach(exo_file) do |line|  
+  aln = Bio::DB::Exonerate::Alignment.parse_custom(line)
+  if aln.identity > min_identity and aln.query_coverage > min_coverage
+	puts aln.line
+  end
+end
+

data/bin/polymarker.rb

@@ -51,6 +51,7 @@ options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
 options[:flanking_size] = 150;
 options[:variation_free_region] = 0 
 options[:extract_found_contigs] = false
+options[:genomes_count] = 3
 options[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 
@@ -71,6 +72,10 @@ OptionParser.new do |opts|
   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("-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
@@ -124,7 +129,7 @@ if 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 "Ragne #{range} is invalid!" unless max > min
+  raise  Bio::DB::Exonerate::ExonerateException.new "Range #{range} is invalid!" unless max > min
   options[:flanking_size] = max
 end
 
@@ -214,7 +219,8 @@ File.open(test_file) do | f |
       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.genomes_count = options[:genomes_count]
     snp.snp_in = snp_in
     snp.original_name = original_name
     if snp.position 

data/bio-polyploid-tools.gemspec

@@ -2,19 +2,19 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.6.1 ruby lib
+# stub: bio-polyploid-tools 0.7.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.6.1"
+  s.version = "0.7.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez"]
-  s.date = "2015-03-05"
+  s.date = "2015-05-08"
   s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat"
   s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
-  s.executables = ["bfr.rb", "count_variations.rb", "filter_blat_by_target_coverage.rb", "find_best_blat_hit.rb", "find_best_exonerate.rb", "hexaploid_primers.rb", "homokaryot_primers.rb", "map_markers_to_contigs.rb", "markers_in_region.rb", "polymarker.rb", "snp_position_to_polymarker.rb", "snps_between_bams.rb"]
+  s.executables = ["bfr.rb", "count_variations.rb", "filter_blat_by_target_coverage.rb", "filter_exonerate_by_identity.rb", "find_best_blat_hit.rb", "find_best_exonerate.rb", "hexaploid_primers.rb", "homokaryot_primers.rb", "map_markers_to_contigs.rb", "markers_in_region.rb", "polymarker.rb", "snp_position_to_polymarker.rb", "snps_between_bams.rb"]
   s.extra_rdoc_files = [
     "README",
     "README.md"
@@ -29,6 +29,7 @@ Gem::Specification.new do |s|
     "bin/bfr.rb",
     "bin/count_variations.rb",
     "bin/filter_blat_by_target_coverage.rb",
+    "bin/filter_exonerate_by_identity.rb",
     "bin/find_best_blat_hit.rb",
     "bin/find_best_exonerate.rb",
     "bin/hexaploid_primers.rb",

data/lib/bio/db/exonerate.rb

@@ -18,8 +18,8 @@ module Bio::DB::Exonerate
     query=opts[:query]
  #
 
-    cmdline = "exonerate --verbose 0 --showalignment no --bestn #{opts[:bestn]} --showvulgar no  --model #{opts[:model]}   --ryo '#{opts[:ryo]}' #{query} #{target}"
-    status, stdout, stderr = systemu cmdline
+ cmdline = "exonerate --verbose 0 --showalignment no --bestn #{opts[:bestn]} --showvulgar no  --model #{opts[:model]}   --ryo '#{opts[:ryo]}' #{query} #{target}"
+ status, stdout, stderr = systemu cmdline
     #$stderr.puts cmdline
     if status.exitstatus == 0
       alns = Array.new unless block_given?
@@ -67,45 +67,91 @@ module Bio::DB::Exonerate
       end
     end
 
-    def identity
-      @pi
+    def query
+     unless @query
+       @query = Bio::DB::Fasta::Region.new()
+       @query.entry = query_id 
+       @query.start = query_start + 1
+       @query.end = query_end
+       @query.orientation = query_strand
+       if @query.orientation == :reverse
+        @query.end = query_start 
+        @query.start = query_end + 1
+       end
+       @query
+     end
+     @query
+   end
+
+   def target
+    unless @target
+      @target = Bio::DB::Fasta::Region.new()
+      @target.entry = target_id 
+      @target.start = target_start + 1
+      @target.end = target_end
+      @target.orientation = target_strand
+      if @target.orientation == :reverse
+        @target.end = target_start 
+        @target.start = target_end + 1
+      end
     end
+    @target
+  end
 
-    def parse_sugar(sugar_str)
-      @query_id, @query_start, @query_end, @query_strand, @target_id, @target_start, @target_end, @target_strand, @score = sugar_str.split(/\s+/)
-
-      @query_start  = @query_start.to_i
-      @query_end = @query_end.to_i
-      @target_start = @target_start.to_i
-      @target_end = @target_end.to_i
-      @score = @score.to_f
-
-      if @target_strand == "+"
-        @target_strand = :forward
-      elsif @target_strand == "-"
-        @target_strand = :reverse
-      else
-        raise  ExonerateException.new(), "Ivalid target orientation #{@target_strand} for line:\n#{sugar_str}"
+  def identity
+    @pi
+  end
+  def query_length
+    @ql
+  end
+  def query_coverage
+    total_m = 0
+    vulgar_block.each do |v|  
+      #p v.label
+      if v.label == :M
+        total_m += v.query_length
       end
+    end
+   #puts "Total m #{total_m}"
+   #puts "ql #{query_length}"
+    return 100.00 * total_m.to_f / query_length.to_f 
+  end
 
+  def parse_sugar(sugar_str)
+    @query_id, @query_start, @query_end, @query_strand, @target_id, @target_start, @target_end, @target_strand, @score = sugar_str.split(/\s+/)
 
-      if @query_strand == "+"
-        @query_strand = :forward
-      elsif @query_strand == "-"
-        @query_strand = :reverse
-      else
-        raise  ExonerateException.new(), "Ivalid query orientation #{@query_strand} for line:\n#{sugar_str}"
-      end
+    @query_start  = @query_start.to_i
+    @query_end = @query_end.to_i
+    @target_start = @target_start.to_i
+    @target_end = @target_end.to_i
+    @score = @score.to_f
 
-      raise  ExonerateException.new(), "Inconsistent orientation (forward, query)" if @query_strand == :forward and @query_start > @query_end
-      raise  ExonerateException.new(), "Inconsistent orientation (reverse, query)" if @query_strand == :reverse and @query_start < @query_end
-      raise  ExonerateException.new(), "Inconsistent orientation (forward, target)" if @target_strand == :forward and @target_start > @target_end
-      raise  ExonerateException.new(), "Inconsistent orientation (reverse, target)" if @target_strand == :reverse and @target_start < @target_end
+    if @target_strand == "+"
+      @target_strand = :forward
+    elsif @target_strand == "-"
+      @target_strand = :reverse
+    else
+      raise  ExonerateException.new(), "Ivalid target orientation #{@target_strand} for line:\n#{sugar_str}"
+    end
 
 
-      self
+    if @query_strand == "+"
+      @query_strand = :forward
+    elsif @query_strand == "-"
+      @query_strand = :reverse
+    else
+      raise  ExonerateException.new(), "Ivalid query orientation #{@query_strand} for line:\n#{sugar_str}"
     end
 
+    raise  ExonerateException.new(), "Inconsistent orientation (forward, query)" if @query_strand == :forward and @query_start > @query_end
+    raise  ExonerateException.new(), "Inconsistent orientation (reverse, query)" if @query_strand == :reverse and @query_start < @query_end
+    raise  ExonerateException.new(), "Inconsistent orientation (forward, target)" if @target_strand == :forward and @target_start > @target_end
+    raise  ExonerateException.new(), "Inconsistent orientation (reverse, target)" if @target_strand == :reverse and @target_start < @target_end
+
+
+    self
+  end
+
 
     #The vulgar has to be parsed AFTER the sugar, otherwise it is impossible to determine the orientations
     def parse_vulgar(vulgar_str)
@@ -199,7 +245,7 @@ module Bio::DB::Exonerate
       reg.start = target_snp_pos - flanking_size
       reg.end = target_snp_pos + flanking_size
       raise  ExonerateException.new "Target Query out of bounds!" unless position.between?(query_start, query_end)
-    
+
       reg
     end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.6.1
+  version: 0.7.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-05 00:00:00.000000000 Z
+date: 2015-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -87,6 +87,7 @@ executables:
 - bfr.rb
 - count_variations.rb
 - filter_blat_by_target_coverage.rb
+- filter_exonerate_by_identity.rb
 - find_best_blat_hit.rb
 - find_best_exonerate.rb
 - hexaploid_primers.rb
@@ -110,6 +111,7 @@ files:
 - bin/bfr.rb
 - bin/count_variations.rb
 - bin/filter_blat_by_target_coverage.rb
+- bin/filter_exonerate_by_identity.rb
 - bin/find_best_blat_hit.rb
 - bin/find_best_exonerate.rb
 - bin/hexaploid_primers.rb