bio-svgenes 0.3.1 → 0.3.2

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-svgenes
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-03-05 00:00:00.000000000 Z
+date: 2013-04-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -114,13 +114,13 @@ executables: []
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
-- README.rdoc
+- README.md
 files:
 - .document
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bio-svgenes.gemspec
@@ -133,7 +133,115 @@ files:
 - doc/Bio/Graphics/SVGEE.html
 - doc/Bio/Graphics/Track.html
 - doc/LICENSE_txt.html
+- doc/classes/Bio.html
+- doc/classes/Bio/Graphics.html
+- doc/classes/Bio/Graphics/Glyph.html
+- doc/classes/Bio/Graphics/Glyph.src/M000001.html
+- doc/classes/Bio/Graphics/Glyph.src/M000002.html
+- doc/classes/Bio/Graphics/Glyph.src/M000003.html
+- doc/classes/Bio/Graphics/Glyph.src/M000004.html
+- doc/classes/Bio/Graphics/Glyph.src/M000005.html
+- doc/classes/Bio/Graphics/Glyph.src/M000006.html
+- doc/classes/Bio/Graphics/Glyph.src/M000007.html
+- doc/classes/Bio/Graphics/Glyph.src/M000008.html
+- doc/classes/Bio/Graphics/Glyph.src/M000009.html
+- doc/classes/Bio/Graphics/Glyph.src/M000010.html
+- doc/classes/Bio/Graphics/Glyph.src/M000011.html
+- doc/classes/Bio/Graphics/Glyph.src/M000012.html
+- doc/classes/Bio/Graphics/Glyph.src/M000013.html
+- doc/classes/Bio/Graphics/Glyph.src/M000014.html
+- doc/classes/Bio/Graphics/Glyph.src/M000015.html
+- doc/classes/Bio/Graphics/Glyph.src/M000016.html
+- doc/classes/Bio/Graphics/Glyph.src/M000017.html
+- doc/classes/Bio/Graphics/Glyph.src/M000018.html
+- doc/classes/Bio/Graphics/Glyph.src/M000019.html
+- doc/classes/Bio/Graphics/Glyph.src/M000020.html
+- doc/classes/Bio/Graphics/Glyph.src/M000021.html
+- doc/classes/Bio/Graphics/Glyph.src/M000022.html
+- doc/classes/Bio/Graphics/Glyph.src/M000023.html
+- doc/classes/Bio/Graphics/Glyph.src/M000024.html
+- doc/classes/Bio/Graphics/MiniFeature.html
+- doc/classes/Bio/Graphics/MiniFeature.src/M000001.html
+- doc/classes/Bio/Graphics/MiniFeature.src/M000003.html
+- doc/classes/Bio/Graphics/MiniFeature.src/M000024.html
+- doc/classes/Bio/Graphics/Page.html
+- doc/classes/Bio/Graphics/Page.src/M000010.html
+- doc/classes/Bio/Graphics/Page.src/M000011.html
+- doc/classes/Bio/Graphics/Page.src/M000012.html
+- doc/classes/Bio/Graphics/Page.src/M000013.html
+- doc/classes/Bio/Graphics/Page.src/M000014.html
+- doc/classes/Bio/Graphics/Page.src/M000015.html
+- doc/classes/Bio/Graphics/Page.src/M000016.html
+- doc/classes/Bio/Graphics/Page.src/M000017.html
+- doc/classes/Bio/Graphics/Page.src/M000018.html
+- doc/classes/Bio/Graphics/Page.src/M000019.html
+- doc/classes/Bio/Graphics/Page.src/M000020.html
+- doc/classes/Bio/Graphics/Page.src/M000021.html
+- doc/classes/Bio/Graphics/Page.src/M000022.html
+- doc/classes/Bio/Graphics/Page.src/M000023.html
+- doc/classes/Bio/Graphics/Page.src/M000024.html
+- doc/classes/Bio/Graphics/Page.src/M000025.html
+- doc/classes/Bio/Graphics/Page.src/M000026.html
+- doc/classes/Bio/Graphics/Page.src/M000027.html
+- doc/classes/Bio/Graphics/Page.src/M000028.html
+- doc/classes/Bio/Graphics/Page.src/M000029.html
+- doc/classes/Bio/Graphics/Page.src/M000030.html
+- doc/classes/Bio/Graphics/Page.src/M000031.html
+- doc/classes/Bio/Graphics/Page.src/M000032.html
+- doc/classes/Bio/Graphics/Page.src/M000033.html
+- doc/classes/Bio/Graphics/Page.src/M000034.html
+- doc/classes/Bio/Graphics/Page.src/M000035.html
+- doc/classes/Bio/Graphics/Page.src/M000036.html
+- doc/classes/Bio/Graphics/Page.src/M000037.html
+- doc/classes/Bio/Graphics/Page.src/M000038.html
+- doc/classes/Bio/Graphics/Page.src/M000039.html
+- doc/classes/Bio/Graphics/Page.src/M000040.html
+- doc/classes/Bio/Graphics/Page.src/M000041.html
+- doc/classes/Bio/Graphics/Page.src/M000042.html
+- doc/classes/Bio/Graphics/Page.src/M000043.html
+- doc/classes/Bio/Graphics/Page.src/M000044.html
+- doc/classes/Bio/Graphics/Primitive.html
+- doc/classes/Bio/Graphics/Primitive.src/M000001.html
+- doc/classes/Bio/Graphics/Primitive.src/M000002.html
+- doc/classes/Bio/Graphics/Primitive.src/M000008.html
+- doc/classes/Bio/Graphics/Primitive.src/M000009.html
+- doc/classes/Bio/Graphics/Primitive.src/M000022.html
+- doc/classes/Bio/Graphics/Primitive.src/M000023.html
+- doc/classes/Bio/Graphics/SVGEE.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000002.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000003.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000004.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000005.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000006.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000007.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000008.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000009.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000016.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000017.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000018.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000019.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000020.html
+- doc/classes/Bio/Graphics/SVGEE.src/M000021.html
+- doc/classes/Bio/Graphics/Track.html
+- doc/classes/Bio/Graphics/Track.src/M000001.html
+- doc/classes/Bio/Graphics/Track.src/M000002.html
+- doc/classes/Bio/Graphics/Track.src/M000003.html
+- doc/classes/Bio/Graphics/Track.src/M000004.html
+- doc/classes/Bio/Graphics/Track.src/M000010.html
+- doc/classes/Bio/Graphics/Track.src/M000011.html
+- doc/classes/Bio/Graphics/Track.src/M000012.html
+- doc/classes/Bio/Graphics/Track.src/M000013.html
 - doc/created.rid
+- doc/files/lib/bio-svgenes_rb.html
+- doc/files/lib/bio/graphics/glyph_rb.html
+- doc/files/lib/bio/graphics/mini_feature_rb.html
+- doc/files/lib/bio/graphics/page_rb.html
+- doc/files/lib/bio/graphics/primitive_rb.html
+- doc/files/lib/bio/graphics/svgee_rb.html
+- doc/files/lib/bio/graphics/track_rb.html
+- doc/fr_class_index.html
+- doc/fr_file_index.html
+- doc/fr_method_index.html
 - doc/images/add.png
 - doc/images/arrow_up.png
 - doc/images/brick.png
@@ -166,18 +274,33 @@ files:
 - doc/js/search.js
 - doc/js/search_index.js
 - doc/js/searcher.js
+- doc/manual/bootstrap/css/bootstrap-responsive.css
+- doc/manual/bootstrap/css/bootstrap-responsive.min.css
+- doc/manual/bootstrap/css/bootstrap.css
+- doc/manual/bootstrap/css/bootstrap.min.css
+- doc/manual/bootstrap/img/glyphicons-halflings-white.png
+- doc/manual/bootstrap/img/glyphicons-halflings.png
+- doc/manual/bootstrap/js/bootstrap.js
+- doc/manual/bootstrap/js/bootstrap.min.js
+- doc/manual/img/circle.png
+- doc/manual/img/directed.png
+- doc/manual/img/down_triangle.png
+- doc/manual/img/histogram.png
+- doc/manual/img/span.png
+- doc/manual/img/transcript.png
+- doc/manual/img/up_triangle.png
+- doc/manual/manual.html
+- doc/manual/manual.md
+- doc/rdoc-style.css
 - doc/rdoc.css
 - doc/table_of_contents.html
-- examples/annotate_snps.rb
 - examples/data.txt
 - examples/draw_from_json.rb
-- examples/eg2.rb
 - examples/example.rb
 - examples/example.svg
+- examples/example2.rb
 - examples/example_config.json
 - examples/gene.gff
-- examples/get_coverage_in_windows.rb
-- examples/make_example.rb
 - examples/transcripts.gff
 - lib/bio-svgenes.rb
 - lib/bio/graphics/glyph.rb
@@ -210,7 +333,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1136117613783362089
+      hash: 2365228172068893639
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/README.rdoc

@@ -1,19 +0,0 @@
-= bio-svgenes
-
-Description goes here.
-
-== Contributing to bio-svgenes
- 
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
-* Fork the project
-* Start a feature/bugfix branch
-* Commit and push until you are happy with your contribution
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
-
-== Copyright
-
-Copyright (c) 2012 Dan MacLean. See LICENSE.txt for
-further details.
-

data/examples/annotate_snps.rb

@@ -1,86 +0,0 @@
-#!/usr/bin/env ruby
-#
-#  untitled
-#
-#  Created by Dan MacLean (TSL) on 2012-10-30.
-#  Copyright (c)  . All rights reserved.
-###################################################
-
-require 'ostruct'
-
-class DanGFF
-  attr_accessor :seqname, :source, :attributes, :start, :end, :strand, :feature, :phase, :score
-  
-  def initialize(line)
-    @seqname, @source, @feature, @start, @end, @score, @strand, @phase, @attributes = line.split(/\t/)
-    @start = @start.to_i
-    @end = @end.to_i 
-  end
-
-  def parent
-    self.attributes =~ /Parent=(.*?);/
-    $1
-  end
-  
-  def overlaps?(other)
-    if (self.seqname == other.seqname and self.start >= other.start and self.start <= other.end)
-      return true
-    elsif (self.seqname == other.seqname and self.end >= other.start and self.end <= other.end)
-      return true
-    end
-  end
-  
-  def contains?(other)
-    if self.seqname == other.seqname and self.start <= other.start and self.end >= other.end
-      return true
-    else
-      return false
-    end
-  end
-  
-end
-features_file = ARGV.shift
-bam_file = ARGV.shift
-bgi_snp_file = ARGV.shift
-#rest = data dump files from R
-
-#get SNP list (position, methodd)
-ARGV.each do |file|
-  snps = []
-  file =~ /(.*)_r_dump.csv/
-  id = $1
-  File.open(file,"r").each do |line|
-      next if line=~ /Method/
-      snp = OpenStruct.new
-      snp.index, snp.pos, snp.method =line.chomp.split(/,/)
-      snp.index = snp.index.to_i
-      snp.pos =  snp.pos.to_i
-      snp.seqname = id
-      snp.start = snp.pos
-      snp.end = snp.pos
-      snps << snp
-  end
-  features = []
-  File.open(features_file, "r").each do |line|
-    feature = DanGFF.new(line) 
-    features << feature if feature.seqname == id and feature.feature == "mRNA"
-  end
-
-  features.each do |f|
-    snps.each do |snp|
-      if feature.contains(snp)
-        snp_info = case snp.method
-        when "BGI"
-          get_snp_from_bgi(snp)
-        when "PileUp"
-          get_snp_from_pileup(snp)
-        when "VCF"
-          get_snp_from_vcf(snp)
-        end
-        print snp_out(snp,snp_info)
-      end
-    end
-  end
-  
-end
-

data/examples/eg2.rb

@@ -1,40 +0,0 @@
-#!/usr/bin/env ruby
-#
-#  untitled
-#
-#  Created by Dan MacLean (TSL) on 2012-09-28.
-#  Copyright (c)  . All rights reserved.
-###################################################
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-
-require 'bio-svgenes'
-require 'pp'
-p = Bio::Graphics::Page.new(:width => 800, 
-             :height => 200, 
-             :number_of_intervals => 10)
-             
-             
-
-
-transcript_track_last = p.add_track(:glyph => :transcript, 
-                               :name => 'transcripts (grouped models)', 
-                               :label => true, 
-                               :exon_fill_color => 'green', 
-                               :utr_fill_color => {:type => :radial, :id => :custom, :cx => 5, :cy => 5, :r => 50, :fx => 50, :fy => 50, :stops => [ {:offset => 0, :color => 'rgb(255,255,255)', :opacity => 0},  {:offset => 100, :color => 'rgb(0,127,200)', :opacity => 1},]}, 
-                               :line_color => 'black', 
-                               :feature_height => 20 )
-
-
-feature3 = Bio::Graphics::MiniFeature.new(:start => 3631, 
-                           :end => 5899, 
-                           :strand => '+', 
-                           :exons => [4486,4605,4706,5095,5174,5326], 
-                           :utrs => [3631,4485,5631,5899])
-                           #:utrs => [3631,4276,5439,5899])
-transcript_track_last.add(feature3)
-
-
-p.draw
-
-#pp p

data/examples/get_coverage_in_windows.rb

@@ -1,176 +0,0 @@
-#!/usr/bin/env ruby
-#
-#  get_coverage_in_windows.rb
-#
-#  Created by Dan MacLean (TSL) on 2012-10-05.
-#  Copyright (c)  . All rights reserved.
-###################################################
-require 'optparse'
-require 'pp'
-options = {}
-optparse = OptionParser.new do|opts|
-
-  opts.on( '-b', '--bam FILE', ' name of sorrted BAM file' ) do |b|
-    options[:bam] = b
-
-  end
-  opts.on( '-f', '--reference_file STRING', 'name of the reference sequence fasta file' ) do |f|
-    options[:fasta] = f
- 
-  end
-  opts.on( '-c', '--chromosome STRING', 'name of the chromosome / contig in the fasta file' ) do |c|
-    options[:chrom] = c
-
-  end
-  opts.on( '-s', '--start INT', 'start position)' ) do |s|
-    options[:start] = s.to_i
-
-  end
-  opts.on( '-e', '--stop INT', 'stop position' ) do |e|
-    options[:stop] = e.to_i
-
-  end  
-  opts.on( '-w', '--step INT', 'window size to use' ) do |w|
-    options[:step] = w.to_i
-
-  end  
-  opts.on( '-o', '--bam_opts INT', 'bio-samtools BAM opts' ) do |o|
-    options[:bam_opts] = o ||= {:min_mapping_quality => 20, :min_base_quality => 30}
-
-  end 
-  # This displays the help screen, all programs are
-  # assumed to have this option.
-  opts.on( '-h', '--help', 'Display this screen' ) do
-    puts opts
-    puts %{Example:  ruby get_coverage_in_windows.rb --bam my_bam.bam --reference_file ref.fasta --chromosome contig1 --start 2000 --stop 3000 --step 100 --bam_opts {:min_mapping_quality => 20, :min_base_quality => 20}}
-    exit
-  end
-end
-optparse.parse!
-
-options[:bam_opts] = {:min_mapping_quality => 20}
-
-
-###Actual script --- 
-require 'rubygems'
-require 'bio-samtools'
-require 'enumerator'
-bam = Bio::DB::Sam.new({:bam=>options[:bam], :fasta=>options[:fasta]} )
-bam.open
-
-def passes_quality(aln, options)
-  if aln.mapq > options[:bam_opts][:min_mapping_quality] && aln.is_mapped
-    true
-  else 
-    false
-  end
-end
-
-def actually_modify(cigar_arr, bases_to_ignore_at_start)
-  result = []
-  bases_ditched = 0
-  cigar_arr.each do |arr|
-    if arr[0] < bases_to_ignore_at_start - bases_ditched
-      bases_ditched += arr[0]
-    elsif arr[0] + bases_ditched >= bases_to_ignore_at_start && bases_ditched < bases_to_ignore_at_start
-      remainder = arr[0] - (bases_to_ignore_at_start - bases_ditched)
-      bases_ditched += (bases_to_ignore_at_start - bases_ditched)
-      result << [remainder, arr[1]] unless remainder == 0
-    elsif bases_ditched >= bases_to_ignore_at_start
-      result << [arr[0],arr[1]]
-    else
-      raise "Shouldn't ever happen. Did though... Panic. Alarums. Etc."
-      exit
-    end
-  end
-  result
-end
-
-def correct_cigar_for_overlaps(cigar_arr, bases_to_ignore_at_start, bases_to_ignore_at_end)
-  #takes the end off the cigar arr if the bases it describes are outside the window
-  return cigar_arr if bases_to_ignore_at_start == 0 && bases_to_ignore_at_end == 0
-  result = actually_modify(cigar_arr,bases_to_ignore_at_start)
-  actually_modify(result.reverse, bases_to_ignore_at_end).reverse
-end
-
-(options[:start]..options[:stop]).step(options[:step]) do |start|
-  positions = Array.new(options[:step], 0.0)
-
-  bam.fetch(options[:chrom], start, start + options[:step]).each do |aln|
-    next unless passes_quality(aln, options)
-    
-    #update start and end for overhanging clipped bases
-    a = aln.cigar.split(/([A-Z])/)
-    cigar_arr = a.enum_for(:each_slice, 2).to_a #convert to array of arrays
-    cigar_arr.collect!{|a| [a.first.to_i, a.last] } #convert numbers to ints
-    if cigar_arr.first.last == "S" or cigar_arr.first.last == "H"
-      aln.pos = aln.pos - cigar_arr.first.first
-      aln.pos = 1 if aln.pos < 1 #ignore negative overhangs...
-    end
-    
-    if cigar_arr.last.last == "S" or cigar_arr.last.last == "H" 
-      aln.calend = aln.calend - cigar_arr.last.first
-      aln.calend = 1 if aln.calend < 1
-    end
-    
-    ##remove any padding operations, we're only concerned with alignments relative to the reference, not other reads.. 
-    cigar_arr.delete_if {|b| b.last == "P"}
-    #need to know whether start outside window ...
-    bases_to_ignore_at_start = 0
-    bases_to_ignore_at_end = 0
-    
-    if aln.pos < start
-      bases_to_ignore_at_start = start - aln.pos
-    end
-    
-    if aln.calend >= start + options[:step] ## left hand border is included in window, right hand border excluded
-      bases_to_ignore_at_end = aln.calend - (start + options[:step]) + 1
-    end
-    
-    cigar_arr = correct_cigar_for_overlaps(cigar_arr.dup, bases_to_ignore_at_start, bases_to_ignore_at_end)
-    #puts "start ignore = #{bases_to_ignore_at_start}"
-    #puts "end ignore = #{bases_to_ignore_at_end}"
-    #modify the read objects start and stop positions to keep only the bit in the window
-    #ignore soft clipping at the start and end
-    if bases_to_ignore_at_start >0
-      aln.pos = aln.pos + bases_to_ignore_at_start
-    end
-    if bases_to_ignore_at_end > 0
-      aln.calend = aln.calend - bases_to_ignore_at_end
-    end
-    
-     begin
-       raise "aln start >= aln end" if aln.pos > aln.calend 
-     rescue
-       next
-     else
-      read_start_corrected = aln.pos - start
-      read_end_corrected = aln.calend - start
-      range_start = read_start_corrected
-      range_stop =  read_end_corrected
-      positions[range_start..range_stop] = positions.slice(range_start..range_stop).collect! {|a| a += 1}
-      ranges_to_decrement = []
-      dist_through_read = 0
-      cigar_arr.each_with_index do |cigar,i|
-      #use the corrected cigar array to correct the coverage post-hoc
-       if cigar.last == "D" or cigar.last == "N"
-         ranges_to_decrement << Range.new(read_start_corrected + dist_through_read, read_start_corrected + dist_through_read + cigar.first - 1)
-       end
-       dist_through_read += cigar.first
-      end #end cigar_arr each
-      #pp ranges_to_decrement unless ranges_to_decrement.empty?
-      ranges_to_decrement.each do |range|
-        begin
-          positions[range] = positions.slice(range).collect! {|b| b -= 1}
-        rescue
-          puts "Error: positions array likely  out of range ... this error affects one read only ... so we'll skip it. Panic if you get lots of this"
-        end
-      end
-     end
-  end #end fetch
-  average = positions.inject(0) {|r,e|  r + e} / positions.length.to_f
-  puts [start, start + options[:step], average].join("\t")
-
-end
-
-bam.close