Module: Circola

Defined in:
lib/circola.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.clean_up(files) ⇒ Object 



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# File 'lib/circola.rb', line 135

def Circola.clean_up(files)
  files.each{|f| File.delete f }
end

.make_ideogram(opts) ⇒ Object 



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# File 'lib/circola.rb', line 94

def Circola.make_ideogram(opts)
  opts = {
    :file => nil,
    :default => "2u",
    :pairwise => nil
  }.merge!(opts)
  f = File.open(opts[:file], "w")
  f.puts "<ideogram>\n<spacing>\n#default = {opts[:default]}\n</spacing></ideogram>"
  f.close
  f
end

.pick_color(opts, index) ⇒ Object

gets an array of colour tags from circos conf file, eg. colors.brewer.conf



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# File 'lib/circola.rb', line 59

def Circola.pick_color(opts, index)
  offset = index - ((opts[:colors].length) * (index / opts[:colors].length) )
  opts[:colors][offset]
end

.prep_conf(opts) ⇒ Object 



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# File 'lib/circola.rb', line 106

def Circola.prep_conf(opts)
  opts = {
    :file => nil,
    :chromosomes_units => 1000000,
    :chromosomes_display_default => "yes",
    :karyotype => nil,
    :includes => []
  }.merge!(opts)
  f = File.open(opts[:file], "w")
  [:karyotype, :chromosomes_units, :chromosomes_display_default].each do |par|
    f.puts "#{par} = #{opts[par]}"
  end
  opts[:includes].each do |inc|
    f.puts "<<include #{inc}>>"
  end
  f.close
  f
end

.run_circos(opts) ⇒ Object 



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# File 'lib/circola.rb', line 125

def Circola.run_circos(opts)
  opts = {
    :circos => nil,
    :conf => nil
  }.merge!(opts)
  command = "#{opts[:circos]} -conf #{opts[:conf]}"
  $stderr.puts "executing ... #{command}"
  Kernel.exec(command)
end

Instance Method Details

#each_to_karyotype(opts) ⇒ Object

from any Bio::FlatFile or object iterates through the entries and writes a file in Circos’ karyotype format.

opts: :id => array of [string method, arg1, arg2, … ] to apply to entry_id of Bio::Flatfile entry for Circos id column :label => array of [string method, arg1, arg2, … ] to apply to entry_id of Bio::Flatfile entry for Circos id column :color => array of color strings for Circos color column. Used in order, looped round if too few provided :file => name of file to write to, Defaults to STDOUT if absent or false. returns a File object if written to file



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# File 'lib/circola.rb', line 14

def each_to_karyotype(opts)
  opts = {
    :id => [:gsub, //,""],
    :label => [:gsub, //,""],
    :colors => ['red', 'green', 'blue', 'purple', 'orange'],
    :file => nil
  }.merge!(opts)
  
  #raise TypeError "not a Bio::Flatfile" unless self.is_a?(Bio::FlatFile)
  self.must_be Bio::FlatFile
  file = File.open(opts[:file], "w")
  self.each_with_index do |entry, index|
      id = entry.entry_id.send( *opts[:id] )
      label = entry.entry_id.send( *opts[:label] )
      color = Circola.pick_color(opts, index)#opts[:colors][offset]
      file.puts "chr - #{id} #{label} 0 #{entry.length} #{color}"
  end
  file.close
  file
end

#full_path ⇒ Object

gives the full path of a File object



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# File 'lib/circola.rb', line 83

def full_path
  must_be File
  File.realpath(self.path)
end

#get_color_list ⇒ Object 



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# File 'lib/circola.rb', line 64

def get_color_list
  self.must_be File
  colors = []
  self.each do |line|
    next if line =~ /^[<#\s]/
    colors << line.split(/\s/)[0]
  end
  colors
end

#must_be(type) ⇒ Object 



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# File 'lib/circola.rb', line 74

def must_be type
  begin
    raise "not a #{type}" unless self.is_a?(type)
  rescue Exception => e  
    $stderr.puts e.backtrace
  end
end

#relative_path ⇒ Object

gives relative path from working dir to file



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# File 'lib/circola.rb', line 89

def relative_path
  must_be File
  Pathname.new(self.full_path).relative_path_from(Pathname.new(Dir.pwd)).to_s
end

#text_to_karyotype(opts) ⇒ Object

assumes text file has idtlength



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# File 'lib/circola.rb', line 36

def text_to_karyotype(opts)
  opts = {
    :id => [:gsub, //,""],
    :label => [:gsub, //,""],
    :colors => ['red', 'green', 'blue', 'purple', 'orange'],
    :file => nil
  }.merge!(opts)
  self.must_be File
  file = File.open(opts[:file], "w")
  self.each_with_index do |line, index|
    color = Circola.pick_color(opts, index)
    id,stop = line.chomp.split(/\t/)
    label = id
    id = id.send( *opts[:id] ) 
    label = label.send( *opts[:label] )
    file.puts "chr - #{id} #{label} 0 #{stop} #{color}"
  end
  file.close
  file
end