bio-gngm 0.1.0 → 0.2.0

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/bio-gngm.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-gngm"
-  s.version = "0.1.0"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]
-  s.date = "2012-03-19"
+  s.date = "2012-11-15"
   s.description = "Identify causative mutations in a model genome from NGS reads using the NGM method."
   s.email = "maclean.daniel@gmail.com"
   s.extra_rdoc_files = [
@@ -89,6 +89,7 @@ Gem::Specification.new do |s|
     "examples/use_indels.rb",
     "lib/bio-gngm.rb",
     "lib/bio/util/bio-gngm.rb",
+    "lib/bio/util/mutation_effects.rb",
     "scripts/get_subseq.rb",
     "scripts/make_histograms_laerfyve.rb",
     "scripts/make_histograms_laerfyve_stitched.rb",

data/examples/make_histograms.rb

@@ -14,27 +14,53 @@ $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'bio-gngm'
 require 'bio-samtools'
 
+#def make_snp_array(id, file)
+#  a = []
+#  File.open(file, "r").each do |line|
+#    arr = line.split(/\t/)
+#    next if arr[0] !~ /#{id}/
+#    a << [a]
+#  end
+#end
 
+sequences = Bio::DB::FastaLengthDB.new(:file => ARGV[0])
+$stderr.puts "Loaded sequences..."
 
 
-#open the BAM file and specify the region of interest
-g = Bio::Util::Gngm.new(:file => "aln.bam", 
-               :format => :bam, 
-               :fasta => "reference.fasta", 
-               :samtools => {:r => "Chr1:1-6000000",
+sequences.each do |id, length|
+  g = Bio::Util::Gngm.new(:file => ARGV[1], 
+               #:format => :pileup, 
+               :format => :bam,
+               :fasta => ARGV[0],
+               :chromosome => id,
+               :start => 1,
+               :stop => length,
+               :samtools => {
                              :q => 20,
-                             :Q => 50
-               }
-    )
-#retrieve the SNPs from the BAM file
-g.snp_positions
-
-#plot a frequency histogram for different bin sizes
-[100000, 250000, 500000].each do |bin_width|
-    file_name = "#{bin_width}.png"
+                             :Q => 20
+                             },
+              :variant_call => {
+                 :indels => false, 
+                 :deletions_only => false, 
+                 :insertions_only => false, 
+                 :min_depth => 6, 
+                 :max_depth => 250, 
+                 :mapping_quality => 20.0, 
+                 :min_non_ref_count => 2, 
+                 :ignore_reference_n => true,
+                 :min_snp_quality => 20,
+                 :min_consensus_quality => 20
+                 }               
+  )
+  $stderr.puts "getting #{id}.."
+  
+  g.snp_positions
+  puts "Found #{g.snp_positions.length} SNPs"
+  [100000, 250000, 500000].each do |bin_width|
+    $stderr.puts "working on #{bin_width} windows"
+    file_name = "test_#{id}_#{bin_width}.png"
     g.frequency_histogram("#{file_name}",bin_width)
-end
-
-#close the BAM file
+  end
 g.close
+end
 

data/lib/bio-gngm.rb

@@ -10,3 +10,4 @@
 # was ever to get merged into the main bioruby tree.
 
 require 'bio/util/bio-gngm'
+require 'bio/util/mutation_effects'

data/lib/bio/util/bio-gngm.rb

@@ -5,13 +5,36 @@
 #  Created by Dan MacLean (TSL) on 2011-12-07.
 #  Copyright (c)  . All rights reserved.
 ###################################################
-
+require 'rubygems'
 require 'rinruby'
 require 'bio-samtools'
 require 'bio/db/pileup'
 require 'bio/db/vcf'
 require 'pp'
 
+=begin
+Simple class representing a file of Fasta format sequences and each ones length
+=end
+class Bio::DB::FastaLengthDB
+  require 'bio'
+  def initialize(args)
+    @file = args[:file]
+    @seqs = {}
+    file = Bio::FastaFormat.open(@file)
+    file.each do |entry|
+      @seqs[entry.entry_id] = entry.length
+    end
+    
+    def each
+      @seqs.keys.sort.each do |k|
+        yield k, @seqs[k]
+      end
+    end
+    
+  end
+end
+
+
 =begin
 Extends the methods of the Bio::DB::Pileup class in bio-samtools. A pileup object represents the SAMtools pileup format at 
 http://samtools.sourceforge.net/pileup.shtml. These extension methods are used by the Bio::Util::Gngm object internally and 
@@ -53,11 +76,10 @@ class Bio::DB::Pileup
   # pileup.is_snp?(:min_depth => 5, :min_non_ref_count => 2)
   # pileup.is_snp?(:min_depth => 5, :min_non_ref_count => 1, :ignore_reference_n => true)
   def is_snp?(opts)  
-    if opts[:ignore_reference_n] and self.ref_base == "N" or self.ref_base == "n"
-      return false
-    elsif self.coverage >= opts[:min_depth] and self.non_ref_count >= opts[:min_non_ref_count]
-      return true
-    end
+    return false if self.ref_base == '*'
+    #return false unless is_ct
+    return false if opts[:ignore_reference_n] and self.ref_base == "N" or self.ref_base == "n"
+    return true if self.coverage >= opts[:min_depth] and self.non_ref_count >= opts[:min_non_ref_count]
     false
   end
 end
@@ -131,9 +153,9 @@ class Bio::DB::Vcf
   end
   
   #Returns true if only one variant allele is recorded. Loci with more than one allele are too complicated for now, so are discarded...
-  def has_just_one_variant?
-    self.alternatives.length == 1 and self.variant?
-  end
+  #def has_just_one_variant?
+  #  self.alternatives.length == 1 and self.variant?
+  #end
   
   #Returns true if the position passes criteria
   # 
@@ -143,38 +165,27 @@ class Bio::DB::Vcf
   #- :mapping_quality => 10
   #
   #Example
-  # vcf.pass_quality?(:min_depth => 5, :min_non_ref_count => 2, :mapping_quality => 25)  
+  # vcf.pass_quality?(:min_depth => 5, :min_non_ref_count => 2, :mapping_quality => 25, :min_snp_quality => 20)  
   def pass_quality?(options)
-    (self.used_depth >= options[:min_depth] and self.mq >= options[:mapping_quality] and self.non_ref_allele_count >= options[:min_non_ref_count])
+    (self.used_depth >= options[:min_depth] and self.mq >= options[:mapping_quality] and self.non_ref_allele_count >= options[:min_non_ref_count] and self.qual >= options[:min_snp_quality])
   end
   
-  #Returns true if the length of the alt column is less than that of the ref column in the Vcf and if Vcf.pass_quality? is true.
-  #Looks only at the positions that are predicted simple deletions, any positions where the alt alleles includes more than one deletion or a SNP or an insertion also is ignored.
-  def is_deletion?(options)
-    case
-    when (not self.has_just_one_variant?) then false
-    when  ( self.alt.length < self.ref.length  and self.pass_quality?(options) )  then true
-    else false
-    end
-  rescue ## if something goes wrong, skip the postion, 
+  #returns true if ref col has same length as all alternatives and position variant passes quality
+  def is_mnp?(options)
+    return true if self.alternatives.all? {|x| x.length == self.ref.length} and self.pass_quality?(options)
     false
   end
   
-  #Returns true if the length of the alt column is greater than that of the ref column in the Vcf and if Vcf.pass_quality? is true.
-  #Looks only at the positions that are predicted simple deletions, any positions where the alt alleles includes more than one deletion or a SNP or an insertion also is ignored.
-  def is_insertion?(options)
-      case
-      when (not self.has_just_one_variant?) then false
-      when ( self.alt.length > self.ref.length and self.pass_quality?(options)  ) then true 
-      else false
-      end
-    rescue ## if something goes wrong, skip the postion, 
-      false
+  ##returns true if ref col has length of 1 and is_mnp?
+  def is_snp?(options)
+    return true if self.is_mnp?(options) and self.ref.length == 1
+    false
   end
   
-  #Returns true if either Vcf.is_insertion? or Vcf.is_deletion? is true
-  def is_indel?(opts)
-    self.is_insertion?(opts) || self.is_deletion?(opts)
+  #Returns true if ref col is different in length from any of the entries in alt column
+  def is_indel?(options)
+    return true if self.variant? and self.alternatives.any? {|x| x.length != self.ref.length} and self.pass_quality?(options)
+    false
   end
   
 
@@ -321,19 +332,33 @@ class Gngm
   #
   # g = Bio::Util::Gngm.new(:file => "aln.sort.bam", 
   #             :format => :bam,
-  #             :samtools => {:q => 20, :Q => 50, :r => "Chr1:1-100000"}, 
+  #             :samtools => {:q => 20, :Q => 50}, 
   #             :fasta => "reference.fa"
-  #
+  #             :start => 100,
+  #             :stop => 200
   #  )
   #
   #Required parameters and defaults:
   #- <tt>:file => nil</tt> -the path to the bam file containing the alignments, a .bai index must be present
-  #- <tt>:format => :bam</tt> -always bam
+  #- <tt>:format => :bam</tt> -either :bam, :emap, :pileup (pileup expected to be 10 col format from samtools -vcf)
+  #- <tt>:chromosome => "nil"</tt> -sequence id to look at
+  #- <tt>:start => nil</tt> -start position on that sequence
+  #- <tt>:stop => nil</tt> -stop position on that sequence
   #- <tt>:fasta => nil</tt> -the path to the FASTA formatted reference sequence
-  #- <tt>:samtools => {:q => 20, :Q => 50, :r => "Chr1:100-1100"}</tt> -options for samtools, see bio-samtools documentation for further details. The :r option is required to specify the region of interest 
+  #- <tt>:samtools => {:q => 20, :Q => 50}</tt> -options for samtools, see bio-samtools documentation for further details. The :r option is required to specify the region of interest 
   #Optional parameters and defaults:
+  
   #Most of these are parameters for specific methods and can be over-ridden when particular methods are called
-  #- <tt>:variant_call => {:indels => false, :deletions_only => false, :insertions_only => false, :min_depth => 2, :max_depth => 10000000, :mapping_quality => 10.0, :min_non_ref_count => 2, :ignore_reference_n => true}</tt> -for SNP/Indel calling only one of <tt>:indels, :deletions_only, :insertions_only</tt> should be used.
+  #- <tt>:variant_call => {:indels => false,
+  #                         :min_depth => 2, 
+  #                         :max_depth => 10000000, 
+  #                         :min_snp_quality => 20, 
+  #                         :mapping_quality => 10.0, 
+  #                         :min_non_ref_count => 2, 
+  #                         :ignore_reference_n => true, 
+  #                         :min_consensus_quality => 20, 
+  #                         :min_snp_quality => 20 }</tt>. 
+  #                         For Pileup files from old samtools pileup -vcf <tt>:min_consensus_quality</tt> can be applied
   #- <tt>:threads => {:start => 0.2, :stop => 1.0, :slide => 0.01, :size => 0.1 }</tt> -options for thread windows
   #- <tt>:insert_size_opts => {:ref_window_size => 200, :ref_window_slide => 50, :isize => 150}</tt> -options for insert size calculations
   #- <tt>:histo_bin_width => 250000</tt> -bin width for histograms of SNP frequency
@@ -353,20 +378,30 @@ class Gngm
     @density_max_y = nil #the maximum y value needed to plot the entire set density plots of threads and maintain a consistent scale for plots
     @colours = %w[#A6CEE3 #1F78B4 #B2DF8A #33A02C #FB9A99 #E31A1C #FDBF6F #FF7F00 #CAB2D6 #6A3D9A #FFFF99 #B15928]
     @thread_colours = {}
+    @known_variants = nil #a list of variants to keep track of
     @opts = {
       :file => nil,
       :format => :bam,
       :fasta => nil,
       :samtools => {:q => 20, :Q => 50},
-      ##indels = call any and only indels.. :deletions_only :insertions_only = only one tyoe
+      :indels => false,
+      ##:indels = call indels too, causes return of vcf
+      :insert_size_opts => {:ref_window_size => 200, :ref_window_slide => 50, :isize => 150},
+      :variant_call => { :min_depth => 2, 
+                         :max_depth => 10000000, 
+                         :mapping_quality => 10.0, 
+                         :min_non_ref_count => 2, 
+                         :ignore_reference_n => true, 
+                         :shore_map => false, 
+                         :snp_file => :false, 
+                         :min_consensus_quality => 20, 
+                         :min_snp_quality => 20},
       ## some options are designed to be equivalent to vcfutils.pl from bvftools options when using vcf
       ##:min_depth (-d)
       ##:max_depth (-D)
       ##:mapping_quality (-Q) minimum RMS mappinq quality for SNPs (mq in info fields)
       ##:min_non_ref_count (-a) minimum num of alt bases ... the sum of the last two numbers in DP4 in info fields
       ##doesnt do anything with window filtering or pv values... 
-      :insert_size_opts => {:ref_window_size => 200, :ref_window_slide => 50, :isize => 150},
-      :variant_call => {:indels => false, :deletions_only => false, :insertions_only => false, :min_depth => 2, :max_depth => 10000000, :mapping_quality => 10.0, :min_non_ref_count => 2, :ignore_reference_n => true},
       :histo_bin_width => 250000,
       :graphics => {:width => 1000, :height => 500, :draw_legend => false, :add_boxes => nil},
       :adjust => 1, 
@@ -376,6 +411,7 @@ class Gngm
       :peaks => {:sigma => 3.0, :threshold => 10.0, :background => false, :iterations => 13, :markov => false, :window => 3, :range => 10000} ##range is the width of the box to draw on the peak plot
     }
     @opts.merge!(options)
+    @opts[:samtools][:r] = "#{options[:chromosome]}:#{options[:start]}-#{options[:stop]}"
     open_file
   end
   
@@ -384,6 +420,7 @@ class Gngm
   def open_file
     case @opts[:format]
     when :bam then open_bam
+    when :pileup, :text then open_text
     end
   end
   
@@ -394,6 +431,10 @@ class Gngm
     @file.open
   end
   
+  def open_text
+    @file = File.open(@opts[:file], "r")
+  end
+  
   public
   #for BAM files calls Bio::DB::Sam#close to close the connections to input files safely
   def close
@@ -415,16 +456,31 @@ class Gngm
   #- <tt>:mapping_quality => 10.0</tt> -minimum mapping quality required for a read to be used in depth calculation
   #- <tt>:min_non_ref_count => 2</tt> -minimum number of reads not matching the reference for SNP to be called
   #- <tt>:ignore_reference_n => true</tt> -ignore positions where the reference is N or n
-  # 
+  #- <tt>:shore_map => false</tt> -use SHOREmap INTERVAL calculations as described in Anderson et al., 2009, Nature Methods 6. 8. Requires a file of known SNPs between the mapping line (eg Ler in Andersen et al.,) and a reference line (eg Col in Andersen et al).  
+  #- <tt>:snp_file => -file of known SNPs in format "reference sequence id \t position \t mapping line nucleotide identity \t reference line nucleotide identity". Only used when +:shore_map+ is set to true. Only SNPs listed in this file will be considered.
   #When INDEL calling only one of <tt>:indels, :deletions_only, :insertions_only</tt> should be used. If all are +false+, SNPs are called.
   #
-  #Sets the instance variable @snp_positions. Only gets positions the first time it is called, in subsequent calls pre-computed positions and statistics are returned, so changing parameters has no effect.
+  #calculates or returns the value of the instance variable @snp_positions. Only gets positions the first time it is called, in subsequent calls pre-computed positions and statistics are returned, so changing parameters has no effect.
   def snp_positions(optsa={})
     opts = @opts[:variant_call].merge(optsa)
     return @snp_positions if @snp_positions
-    case
-    when @file.instance_of?(Bio::DB::Sam) then get_snp_positions_from_bam(opts)
+    case @opts[:format]
+    when :bam then get_snp_positions_from_bam(opts)
+    when :text then get_snp_positions_from_text(opts)
+    when :pileup then get_snp_positions_from_pileup(opts)
+    end
+  end
+  
+  ##allows the user to assign SNP positions
+  def snp_positions=(arr)
+    @snp_positions = arr
+  end
+  
+  def is_allowed_substitution?(ref,alt,opts)
+    if opts[:substitutions].instance_of?(Array)
+      return false unless opts[:substitutions].include?("#{ref}:#{alt}")
     end
+    true
   end
   
   private
@@ -432,18 +488,14 @@ class Gngm
   #Sets @snp_positions
   def get_snp_positions_from_bam(options={})
     opts = @opts[:variant_call].merge(options)
-    if opts[:indels] and (opts[:deletions_only] or opts[:insertions_only])
-      raise "Cant have indels and deletions only or insertions only, need to specify ':indels => true' to get both"
-    end
     arr = []
-    ##when we are calling mpileup_plus we need to add :g to the samtools options
-    if opts[:indels] or opts[:deletions_only] or opts[:insertions_only]
-      @opts[:samtools][:g] = true
-    end
+    ##when we are calling mpileup_plus we need to add :g to the samtools options #alw
+    @opts[:samtools][:g] = true if opts[:indels]
+
     
     if not @opts[:samtools][:g]
       @file.mpileup(@opts[:samtools]) do |pileup|
-        arr << [pileup.pos, pileup.discordant_chastity] if pileup.is_snp?(opts)
+        arr << [pileup.pos, pileup.discordant_chastity] if pileup.is_snp?(opts) and is_allowed_substitution?(pileup.ref_base, pileup.consensus,opts)
       end
     else
       @file.mpileup_plus(@opts[:samtools]) do |vcf|
@@ -451,19 +503,56 @@ class Gngm
         next if (opts[:ignore_reference_n] and vcf.ref =~ /N/i)
         ##indel use returns the vcf allele_frequency, not the ChDs (because calculating it is a mess... )
         if opts[:indels]
-          arr << [vcf.pos, vcf.non_ref_allele_freq] if vcf.is_indel?(opts)
-        elsif opts[:deletions_only]
-          arr << [vcf.pos, vcf.non_ref_allele_freq] if vcf.is_deletion?(opts)
-        elsif opts[:insertions_only]
-          arr << [vcf.pos, vcf.non_ref_allele_freq] if vcf.is_insertion?(opts)
+          arr << [vcf.pos, vcf.non_ref_allele_freq] if vcf.is_indel?(opts) and is_allowed_substitution?(vcf.ref, vcf.alt,opts)
+        else
+          arr << [vcf.pos, vcf.non_ref_allele_freq] if vcf.is_snp?(opts) and is_allowed_substitution?(vcf.ref, vcf.alt,opts)
         end
       end
     end
     
     @snp_positions = arr
+
     arr
   end
   
+  private
+  def get_snp_positions_from_map(options={})
+    arr = []
+    opts = @opts[:variant_call].merge(options)
+  end
+  
+  #this does not filter snps, other than to check they are in the right region and are allowed substitutions.. no qual control, assumed to be done prior
+  #text file is of format chr\tpos\tref\talt\tfreq\n
+  def get_snp_positions_from_text(options={})
+    arr = []
+    opts = @opts[:variant_call].merge(options)
+    @file.each do |line|
+        chr,pos,ref,alt,freq = line.chomp.split("\t")
+        pos = pos.to_i
+        freq = freq.to_f
+        next unless chr == @opts[:chromosome] and pos >= @opts[:start] and pos <= @opts[:stop] and is_allowed_substitution?(ref,alt,opts)
+        arr << [pos, freq]
+    end
+    @snp_positions = arr
+  end
+  
+  private 
+  def get_snp_positions_from_pileup(options={})
+    arr = []
+    opts = @opts[:variant_call].merge(options)
+    @file.each do |line|
+      pileup = Bio::DB::Pileup.new(line)
+     if pileup.ref_name != @opts[:chromosome] or pileup.pos < @opts[:start] or pileup.pos > @opts[:stop]
+       next
+     end 
+      #old fashioned 10 col pileup format has extra fields we can use if needed
+     if pileup.is_snp?(opts) and not pileup.consensus_quality.nil? and not pileup.snp_quality.nil?
+       arr << [pileup.pos, pileup.discordant_chastity] if pileup.consensus_quality > opts[:min_consensus_quality] and pileup.snp_quality > opts[:min_snp_quality] and is_allowed_substitution?(pileup.ref_base, pileup.consensus,opts)
+     end
+    end
+    @snp_positions = arr
+  end
+  
   private
   #Gets the insert size for each alignment in the BAM positions from a BAM file according to quality criteria passed by Bio::Util::Gngm#get_insert_size_frequency.
   def get_insert_size_frequency_from_bam(opts={})
@@ -815,7 +904,7 @@ class Gngm
     @peak_indices = nil #needs resetting as we are working with new cluster
     @peak_y_values = nil #needs resetting as we are working with new cluster
     self.calculate_densities(options[:adjust])
-    @clusters = Array.new (@densities.length) {|x| 1 + x}
+    @clusters = Array.new(@densities.length) {|x| 1 + x}
     ##now set the cluster colours.. 
     colours = %w[#A6CEE3 #1F78B4 #B2DF8A #33A02C #FB9A99 #E31A1C #FDBF6F #FF7F00 #CAB2D6 #6A3D9A #FFFF99 #B15928]
     ci = 0
@@ -916,7 +1005,7 @@ class Gngm
     r.quit
   end
   
-  private
+  #private
   #Calculates the position of peaks in the signal curve
   def get_peaks(opts=@opts[:peaks])
     opts[:background] = opts[:background].to_s.upcase
@@ -1023,7 +1112,29 @@ class Gngm
     return r
   end
   
+  private
+  #returns an array of arrays of known variants
+  #file:
+  #chr1	500	A	G
+  #chr2	1000	ATGTTA
+  #chr3	1500	.	TTGGA 
+  # returns [["chr1", "500", "A", "G"], ["chr2", "1000", "ATG", "TTA"], ["chr3", "1500", ".", "TTGGA"]]
+  def parse_known_variants(file)
+    File.open(file, "r").readlines.collect {|x| x.chomp.split("\t")}
+  end
 
+  public
+  #Deletes everything from self.snp_positions not mentioned by position in self.known_variants. Directly modifies self.snp_positions
+  def keep_known_variants(file=nil)
+    raise "file of known variants not provided and @known_variants is nil" if @known_variants.nil? and file.nil?
+    @known_variants = parse_known_variants(file) if @known_variants.nil? and file
+    @snp_positions.each do |snp|
+    end
+  end
+  
 end
 end
 end
+
+
+

data/lib/bio/util/mutation_effects.rb

@@ -0,0 +1,39 @@
+require 'bio'
+
+
+module Bio
+  class Util
+    def self.read_gff3(fn)
+      genearray=Array.new
+      mRNAhash=Hash.new
+      exonhash=Hash.new
+      tehash=Hash.new
+      lastid = ''
+      lastrecord = nil
+      gff3 = Bio::GFF::GFF3.new(File.read(fn))
+      gff3.records.each do | record |
+       feature_type = record.feature_type
+       if(feature_type == 'gene')
+         genearray << record.id
+       elsif(feature_type == 'mRNA')
+         parent = record.get_attribute('Parent')
+        if mRNAhash[parent] == nil
+          mRNAhash[parent] = [record]
+        else 
+          mRNAhash[parent] << record
+        end
+       elsif(feature_type == 'transposable_element')
+        #--- not yet implemented
+       elsif(feature_type == 'exon')
+        parents = record.get_attributes('Parent')
+        parents.each do |parent|
+         if exonhash[parent] == nil
+          exonhash[parent] = Array.new
+         end
+         exonhash[parent] << record
+         end
+       end
+      end
+    end
+  end
+end

data/scripts/make_threads_unmapped_simulation.rb

@@ -14,36 +14,48 @@ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'bio-gngm'
 require 'bio'
+require 'pp'
 length = 0
 chr_name = "" 
-file = Bio::FastaFormat.open("/Users/macleand/Desktop/deletion_simulation/NC_000962.fna")
-file.each do |entry|
-  length = entry.length
-  chr_name = entry.entry_id
-end
+#file = Bio::FastaFormat.open("/Users/macleand/Desktop/deletion_simulation/NC_000962.fna")
+#file.each do |entry|
+#  length = entry.length
+#  chr_name = entry.entry_id
+#end
 
 
-  region = "gi|57116681|ref|NC_000962.2|:1-#{length}"
+  region = "1:2000000-3000000"
   
   puts "analyzing - #{region}"
 
-  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/deletion_simulation/aln.sort.bam", 
+  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/insertion_finding/athal/aln.sort.bam", 
                :format => :bam, 
-               :fasta => "/Users/macleand/Desktop/deletion_simulation/NC_000962.fna",
-               :samtools => {:q => 20, :Q => 50, :r => region
+               :fasta => "/Users/macleand/Desktop/insertion_finding/athal/chr1.fa",
+               :samtools => {:q => 50, :Q => 13, :r => region
                }
     )
       
-      g.get_unmapped_mate_frequency(:ref_window_size => 76, :ref_window_slide => 76)
-      g.collect_threads(:start => 0.0, :stop => 0.5, :slide => 0.1, :size => 0.1)
-      puts g.threads
+      g.get_unmapped_mate_frequency(:ref_window_size => 152, :ref_window_slide => 10)
+      
+      
+      
+      g.collect_threads(:start => 0.0, :stop => 1.0, :slide => 0.1, :size => 0.1)
+      pp g.threads
+      g.threads.delete_if {|x| x.last.length <= 3 }
 
       begin
-        g.calculate_clusters(:pseudo => true)
-        filename = "sim_2_#{region}_all_threads.png" 
-        g.draw_threads(filename, :draw_legend => "sim_#{region}_legend.png")
+        #g.calculate_clusters(:pseudo => true)
+        g.calculate_clusters(:k => 4, :adjust => 0.5, :control_chd => 0.0, :expected_chd => 0.3, :pseudo => false)
+        filename = "deletion_real_data#{region}_all_threads.png" 
+        g.draw_threads(filename, :draw_legend => "deletion_real_data#{region}_legend.png")
         ##no bands or signal to draw without clustering... 
-        filename = "sim_#{region}_hits.png"
+        filename = "deletion_real_data#{region}_bands.png"
+        g.draw_bands(filename)
+        filename = "deletion_real_data#{region}_signal.png"
+        g.draw_signal(filename)
+        
+        
+        filename = "deletion_real_data_#{region}_hits.png"
         g.draw_hit_count(filename)
       rescue  Exception => e
         puts e.message, e.backtrace

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gngm
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-19 00:00:00.000000000 Z
+date: 2012-11-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70226478302620 !ruby/object:Gem::Requirement
+  requirement: &70148237802860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *70226478302620
+  version_requirements: *70148237802860
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &70226478299960 !ruby/object:Gem::Requirement
+  requirement: &70148237802000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *70226478299960
+  version_requirements: *70148237802000
 - !ruby/object:Gem::Dependency
   name: rinruby
-  requirement: &70226478297240 !ruby/object:Gem::Requirement
+  requirement: &70148237801440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 2.0.2
   type: :runtime
   prerelease: false
-  version_requirements: *70226478297240
+  version_requirements: *70148237801440
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &70226478383720 !ruby/object:Gem::Requirement
+  requirement: &70148237800620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70226478383720
+  version_requirements: *70148237800620
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70226478382700 !ruby/object:Gem::Requirement
+  requirement: &70148237793360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *70226478382700
+  version_requirements: *70148237793360
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70226478381080 !ruby/object:Gem::Requirement
+  requirement: &70148237791880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70226478381080
+  version_requirements: *70148237791880
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &70226478380320 !ruby/object:Gem::Requirement
+  requirement: &70148237789480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70226478380320
+  version_requirements: *70148237789480
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70226478379680 !ruby/object:Gem::Requirement
+  requirement: &70148237788820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *70226478379680
+  version_requirements: *70148237788820
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &70226478379180 !ruby/object:Gem::Requirement
+  requirement: &70148237788260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
         version: 0.5.0
   type: :development
   prerelease: false
-  version_requirements: *70226478379180
+  version_requirements: *70148237788260
 - !ruby/object:Gem::Dependency
   name: rinruby
-  requirement: &70226478378620 !ruby/object:Gem::Requirement
+  requirement: &70148237787540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,10 +120,10 @@ dependencies:
         version: 2.0.2
   type: :development
   prerelease: false
-  version_requirements: *70226478378620
+  version_requirements: *70148237787540
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &70226478378060 !ruby/object:Gem::Requirement
+  requirement: &70148237787000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -131,7 +131,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70226478378060
+  version_requirements: *70148237787000
 description: Identify causative mutations in a model genome from NGS reads using the
   NGM method.
 email: maclean.daniel@gmail.com
@@ -213,6 +213,7 @@ files:
 - examples/use_indels.rb
 - lib/bio-gngm.rb
 - lib/bio/util/bio-gngm.rb
+- lib/bio/util/mutation_effects.rb
 - scripts/get_subseq.rb
 - scripts/make_histograms_laerfyve.rb
 - scripts/make_histograms_laerfyve_stitched.rb
@@ -260,7 +261,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3948590901607660961
+      hash: 729394422036910323
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: