bio-gngm 0.1.0

data/scripts/get_subseq.rb

@@ -0,0 +1,16 @@
+#!/usr/bin/env ruby
+#
+#  untitled
+#
+#  Created by Dan MacLean (TSL) on 2012-03-01.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+require 'bio'
+
+file = Bio::FastaFormat.open(ARGV[0])
+file.each do |entry|
+  section = entry.seq[ARGV[1].to_i..ARGV[2].to_i]
+  puts ">#{entry.entry_id}:#{ARGV[1]}..#{ARGV[2]}"
+  puts section
+end

data/scripts/make_histograms_laerfyve.rb

@@ -0,0 +1,83 @@
+#!/usr/bin/env ruby
+#
+#  make_histograms
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions and make histograms
+### of the frequncy of discordant SNPs. Generates plots for each. 
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio-samtools'
+require 'bio'
+=begin
+module Bio
+  class DB
+    class Sam
+      def each_reference
+        index_stats.each_pair do |k, v|
+          yield k, v[:length].to_i
+        end
+      end
+    end
+  end
+end
+=end
+
+#ff = Bio::FlatFile.new(Bio::FastaFormat, "/Users/macleand/Desktop/laerfyfe_vs_ler/Ler-1.SHORE.scaffolds.2010-09-30.500bp.fa")
+file = Bio::FastaFormat.open("/Users/macleand/Desktop/laerfyfe_vs_ler/Ler-1.SHORE.scaffolds.2010-09-30.500bp.fa")
+file.each do |entry|
+    next if entry.length < 10000
+    $stderr.puts "doing #{entry.entry_id} - #{entry.length}"                      
+    g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/laerfyfe_vs_ler/aln.sort.bam", 
+                 :format => :bam,
+                 :samtools => {:q => 20, :Q => 50, :r => "#{entry.entry_id}:1-#{entry.length}"}, 
+                 :fasta => "/Users/macleand/Desktop/laerfyfe_vs_ler/Ler-1.SHORE.scaffolds.2010-09-30.500bp.fa"
+
+      )
+       g.snp_positions(:min_depth => 10, :mapping_quality => 40.0, :min_non_ref_count => 5)
+          puts "found #{g.snp_positions.length} SNPs .."
+          begin
+          [1000, 2500, 5000, 10000, 25000, 50000].each do |bin_width|
+            next if bin_width > entry.length
+            file_name = "ler_contigs_#{entry.entry_id}_#{bin_width}.png"
+            g.frequency_histogram("#{file_name}",bin_width)
+          end
+          rescue Exception => e
+            puts "failed #{e}"
+          ensure 
+            g.close
+          end
+end
+#sam = Bio::DB::Sam.new(:bam => "/Users/macleand/Desktop/laerfyfe_vs_ler/aln.sort.bam", 
+#                      :fasta => "/Users/macleand/Desktop/laerfyfe_vs_ler/Ler-1.SHORE.scaffolds.2010-09-30.500bp.fa")
+#sam.open                      
+#sam.fetch("Scaffold_2", 10000, 10500).each do |a|
+#  puts a.qname
+#end
+
+#sam.close
+#sam.each_reference do |name, length|
+#  $stderr.puts "skipping..."
+#  next if length < 10000
+#  $stderr.puts "doing #{name}"                      
+#  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/laerfyfe_vs_ler/aln.sort.bam", 
+#               :format => :bam,
+#               :samtools => {:q => 20, :Q => 50}, 
+#               :fasta => "/Users/macleand/Desktop/laerfyfe/Ler-1.SHORE.scaffolds2010-09-30.bp.fa"
+  
+#    )
+#    g.snp_positions(:min_depth => 10, :mapping_quality => 40.0, :min_non_ref_count => 5)
+    #puts g.snp_positions.length
+    
+#    [10000, 25000, 50000, 100000, 250000, 500000].each do |bin_width|
+#      file_name = "ler_contigs_#{name}_#{bin_width}.png"
+#      g.frequency_histogram("#{file_name}",bin_width)
+#    end
+#    g.close
+#end
+#sam.close

data/scripts/make_histograms_laerfyve_stitched.rb

@@ -0,0 +1,59 @@
+#!/usr/bin/env ruby
+#
+#  make_histograms
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions and make histograms
+### of the frequncy of discordant SNPs. Generates plots for each. 
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio-samtools'
+require 'bio'
+#!/usr/bin/env ruby
+#
+#  make_histograms
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions and make histograms
+### of the frequncy of discordant SNPs. Generates plots for each. 
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio-samtools'
+require 'bio'
+
+length = 0
+chr_name = "" 
+file = Bio::FastaFormat.open("/Users/macleand/Desktop/laerfyve_vs_stitched_ler/ler_contigs_stitched.fa"
+file.each do |entry|
+  length = entry.length
+  chr_name = entry.entry_id
+end
+
+
+
+  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/laerfyve_vs_stitched_ler/aln.sort.bam", 
+               :format => :bam,
+               :samtools => {:q => 20, :Q => 50, :r => "#{chr_name}:1-#{length}"}, 
+               :fasta => "/Users/macleand/Desktop/laerfyve_vs_stitched_ler/ler_contigs_stitched.fa"
+  
+    )
+    g.snp_positions(:min_depth => 10, :mapping_quality => 40.0, :min_non_ref_count => 5)
+    puts g.snp_positions.length
+    
+    [10000, 25000, 50000, 100000, 250000, 500000].each do |bin_width|
+      file_name = "stitched_contigs_snps_q_filt_#{bin_width}.png"
+      g.frequency_histogram("#{file_name}",bin_width)
+    end
+    g.close
+
+

data/scripts/make_threads_isize_laerfyfe.rb

@@ -0,0 +1,52 @@
+#!/usr/bin/env ruby
+#
+#  make_bands
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions, make density threads for different kernels, 
+### cluster for different values of k and then draw the threads, bands and signal. Generates plots for each new set of parameters 
+
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio'
+length = 0
+chr_name = "" 
+file = Bio::FastaFormat.open("/Users/macleand/Desktop/laerfyve_vs_stitched_ler/ler_contigs_stitched.fa")
+file.each do |entry|
+  length = entry.length
+  chr_name = entry.entry_id
+end
+
+puts chr_name
+  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/laerfyve_vs_stitched_ler/aln.sort.bam", 
+               :format => :bam, 
+               :fasta => "/Users/macleand/Desktop/laerfyve_vs_stitched_ler/ler_contigs_stitched.fa",
+               :samtools => {:q => 20, :Q => 50, :r => "#{chr_name}:1-#{length}"
+               }
+    )
+      
+      g.get_insert_size_frequency(:ref_window_size => 750, :ref_window_slide => 750, :isize => 184)
+      g.collect_threads
+      [0.25, 0.5, 1.0].each do |kernel_adjust|
+        [4, 9, 11].each do | k |
+          begin
+              g.calculate_clusters(:k => k, :adjust => kernel_adjust, :control_chd => 0.5, :expected_chd => 0.2)
+              filename = "isize_#{k}_#{kernel_adjust}_all_threads.png" 
+              g.draw_threads(filename, :draw_legend => "isize_#{k}_#{kernel_adjust}_legend.png")
+              filename = "isize_#{k}_#{kernel_adjust}_bands.png"
+              g.draw_bands(filename)
+              filename = "isize_#{k}_#{kernel_adjust}_signal.png"
+              g.draw_signal(filename)
+              filename = "isize_#{k}_#{kernel_adjust}_hits.png"
+              g.draw_hit_count(filename)
+            rescue  Exception => e
+                puts "failed on #{k} #{kernel_adjust}"
+                puts e.message, e.backtrace
+            end
+          end
+        end

data/scripts/make_threads_unmapped_laerfyfe.rb

@@ -0,0 +1,72 @@
+#!/usr/bin/env ruby
+#
+#  make_bands
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions, make density threads for different kernels, 
+### cluster for different values of k and then draw the threads, bands and signal. Generates plots for each new set of parameters 
+
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio'
+length = 0
+chr_name = "" 
+file = Bio::FastaFormat.open("/Users/macleand/Desktop/laerfyve_vs_stitched_ler/ler_contigs_stitched.fa")
+file.each do |entry|
+  length = entry.length
+  chr_name = entry.entry_id
+end
+
+ctrl_thread_values = []
+expected_thread_values = []
+interval_width = 10000000
+#puts chr_name
+(1..length).step(interval_width) do |start|
+  stop = start + interval_width
+  region = "#{chr_name}:#{start}-#{stop}"
+  
+  puts "analyzing - #{region}"
+
+  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/laerfyve_vs_stitched_ler/aln.sort.bam", 
+               :format => :bam, 
+               :fasta => "/Users/macleand/Desktop/laerfyve_vs_stitched_ler/ler_contigs_stitched.fa",
+               :samtools => {:q => 20, :Q => 50, :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
+      [0.5].each do |kernel_adjust|
+        [4].each do | k |
+          begin  
+              g.calculate_clusters(:k => k, :adjust => kernel_adjust, :control_chd => 0.0, :expected_chd => 0.4, :pseudo => false)
+              #filename = "unmapped_2_#{region}_#{k}_#{kernel_adjust}_all_threads.png" 
+              #g.draw_threads(filename, :draw_legend => "unmapped_#{region}_#{k}_#{kernel_adjust}_legend.png")
+              ctrl_threads = g.get_band(0.0)
+              expected_threads = g.get_band(0.4)
+              ctrl_thread_values += g.threads.select {|x| ctrl_threads.include?(x.first) }.last
+              expected_thread_values += g.threads.select {|x| expected_threads.include?(x.first) }.last
+              filename = "unmapped_2_#{region}_#{k}_#{kernel_adjust}_bands.png"
+              g.draw_bands(filename)
+              #filename = "unmapped_#{region}_#{k}_#{kernel_adjust}_signal.png"
+              #g.draw_signal(filename)
+              #filename = "unmapped_#{region}_#{k}_#{kernel_adjust}_hits.png"
+              #g.draw_hit_count(filename)
+
+          rescue  Exception => e
+                puts "failed on #{k} #{kernel_adjust}"
+                puts e.message, e.backtrace
+          end
+        end
+      end
+    g.close      
+
+    
+end
+File.open("ctrl_thread.txt", 'w') {|f| f.write(ctrl_thread_values.join("\n")) }
+File.open("epxected_thread.txt", 'w') {|f| f.write(expected_thread_values.join("\n")) }

data/scripts/make_threads_unmapped_laerfyfe_pseudo.rb

@@ -0,0 +1,56 @@
+#!/usr/bin/env ruby
+#
+#  make_bands
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions, make density threads for different kernels, 
+### cluster for different values of k and then draw the threads, bands and signal. Generates plots for each new set of parameters 
+
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio'
+length = 0
+chr_name = "" 
+file = Bio::FastaFormat.open("/Users/macleand/Desktop/laerfyfe_vs_ler/Ler-1.SHORE.scaffolds.2010-09-30.500bp.fa")
+file.each do |entry|
+  length = entry.length
+  chr_name = entry.entry_id
+
+
+interval_width = 5000000
+puts chr_name
+#(1..length).step(interval_width) do |start|
+  #stop = start + interval_width
+  region = "#{chr_name}:#{1}-#{length}"
+  file = chr_name
+  
+  puts "analyzing - #{region}"
+
+  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/laerfyfe_vs_ler/aln.sort.bam", 
+               :format => :bam, 
+               :fasta => "/Users/macleand/Desktop/laerfyfe_vs_ler/Ler-1.SHORE.scaffolds.2010-09-30.500bp.fa",
+               :samtools => {:q => 20, :Q => 50, :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)
+
+          begin
+              g.calculate_clusters(:pseudo => true)
+              filename = "unmapped_#{file}_all_threads.png" 
+              g.draw_threads(filename, :draw_legend => "unmapped_#{file}_legend.png")
+              ##no bands or signal to draw without clustering... 
+              filename = "unmapped_#{file}_hits.png"
+              g.draw_hit_count(filename)
+            rescue  Exception => e
+                puts e.message, e.backtrace
+            end
+
+ #end       
+end

data/scripts/make_threads_unmapped_simulation.rb

@@ -0,0 +1,54 @@
+#!/usr/bin/env ruby
+#
+#  make_bands
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions, make density threads for different kernels, 
+### cluster for different values of k and then draw the threads, bands and signal. Generates plots for each new set of parameters 
+
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio'
+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
+
+
+  region = "gi|57116681|ref|NC_000962.2|:1-#{length}"
+  
+  puts "analyzing - #{region}"
+
+  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/deletion_simulation/aln.sort.bam", 
+               :format => :bam, 
+               :fasta => "/Users/macleand/Desktop/deletion_simulation/NC_000962.fna",
+               :samtools => {:q => 20, :Q => 50, :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
+
+      begin
+        g.calculate_clusters(:pseudo => true)
+        filename = "sim_2_#{region}_all_threads.png" 
+        g.draw_threads(filename, :draw_legend => "sim_#{region}_legend.png")
+        ##no bands or signal to draw without clustering... 
+        filename = "sim_#{region}_hits.png"
+        g.draw_hit_count(filename)
+      rescue  Exception => e
+        puts e.message, e.backtrace
+      end
+
+
+
+        

data/scripts/make_threads_unmapped_simulation_immediate_region.rb

@@ -0,0 +1,59 @@
+#!/usr/bin/env ruby
+#
+#  make_bands
+#
+#  Created by Dan MacLean (TSL) on 2012-01-17.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+### An example script to loop over each reference in the BAM file, get SNP positions, make density threads for different kernels, 
+### cluster for different values of k and then draw the threads, bands and signal. Generates plots for each new set of parameters 
+
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gngm'
+require 'bio'
+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
+
+
+  region = "gi|57116681|ref|NC_000962.2|:1010000-1020000"
+  
+  puts "analyzing - #{region}"
+
+  g = Bio::Util::Gngm.new(:file => "/Users/macleand/Desktop/deletion_simulation/aln.sort.bam", 
+               :format => :bam, 
+               :fasta => "/Users/macleand/Desktop/deletion_simulation/NC_000962.fna",
+               :samtools => {:q => 20, :Q => 50, :r => region
+               }
+    )
+      
+      g.get_unmapped_mate_frequency(:ref_window_size => 76, :ref_window_slide => 76)
+      g.collect_threads
+      puts g.snp_positions
+=begin
+      [0.25, 0.5, 1.0].each do |kernel_adjust|
+        [4, 9, 11].each do | k |
+          begin
+              g.calculate_clusters(:k => k, :adjust => kernel_adjust, :control_chd => 1.0, :expected_chd => 0.5, :pseudo => false)
+              filename = "sim_#{region}_#{k}_#{kernel_adjust}_all_threads.png" 
+              g.draw_threads(filename, :draw_legend => "unmapped_#{region}_#{k}_#{kernel_adjust}_legend.png")
+              filename = "sim_#{region}_#{k}_#{kernel_adjust}_bands.png"
+              g.draw_bands(filename)
+              filename = "sim_#{region}_#{k}_#{kernel_adjust}_signal.png"
+              g.draw_signal(filename)
+              filename = "sim_#{region}_#{k}_#{kernel_adjust}_hits.png"
+              g.draw_hit_count(filename)
+            rescue  Exception => e
+                puts "failed on #{k} #{kernel_adjust}"
+                puts e.message, e.backtrace
+            end
+          end
+        end
+=end