barmcakes 0.0.6 → 0.0.11

data/lib/barmcakes.rb

@@ -1,2 +1,4 @@
 require 'arrghs'
-require 'file'
+require 'file'
+require 'circola'
+require 'bio_tools'

data/lib/bio_tools.rb

@@ -0,0 +1,23 @@
+  
+class Bio::DB::FastaLengthDB
+    require 'bio'
+
+    def initialize(fasta)
+      @file = fasta
+      @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
+
+      def [] (key)
+        @seqs[key]
+      end
+    end
+end

data/lib/circola.rb

@@ -0,0 +1,141 @@
+require 'bio'
+require 'pathname'
+
+module Circola
+  #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
+  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
+  
+  #assumes text file has id\tlength
+  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
+  
+  #gets an array of colour tags from circos conf file, eg. colors.brewer.conf
+  
+  def Circola.pick_color(opts, index)
+    offset = index - ((opts[:colors].length) * (index / opts[:colors].length) )
+    opts[:colors][offset]
+  end
+  
+  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
+  
+  def must_be type
+    begin
+      raise "not a #{type}" unless self.is_a?(type)
+    rescue Exception => e  
+      $stderr.puts e.backtrace
+    end
+  end
+  
+  #gives the full path of a File object
+  def full_path
+    must_be File
+    File.realpath(self.path)
+  end
+  
+  #gives relative path from working dir to file
+  def relative_path
+    must_be File
+    Pathname.new(self.full_path).relative_path_from(Pathname.new(Dir.pwd)).to_s
+  end
+ 
+  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
+ 
+  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
+  
+  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
+  
+  def Circola.clean_up(files)
+    files.each{|f| File.delete f }
+  end
+  
+end
+
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: barmcakes
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.11
   prerelease: 
 platform: ruby
 authors:
@@ -21,6 +21,8 @@ files:
 - lib/barmcakes.rb
 - lib/arrghs.rb
 - lib/file.rb
+- lib/circola.rb
+- lib/bio_tools.rb
 homepage: http://github.com/danmaclean/barmcakes
 licenses: []
 post_install_message: