barmcakes 0.0.6 → 0.0.11
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- data/lib/barmcakes.rb +3 -1
- data/lib/bio_tools.rb +23 -0
- data/lib/circola.rb +141 -0
- metadata +3 -1
data/lib/barmcakes.rb
CHANGED
data/lib/bio_tools.rb
ADDED
@@ -0,0 +1,23 @@
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2
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class Bio::DB::FastaLengthDB
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3
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require 'bio'
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4
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5
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def initialize(fasta)
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6
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@file = fasta
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7
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@seqs = {}
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8
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file = Bio::FastaFormat.open(@file)
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9
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file.each do |entry|
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10
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@seqs[entry.entry_id] = entry.length
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11
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end
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12
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def each
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14
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@seqs.keys.sort.each do |k|
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yield k, @seqs[k]
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end
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end
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def [] (key)
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@seqs[key]
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end
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end
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end
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data/lib/circola.rb
ADDED
@@ -0,0 +1,141 @@
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require 'bio'
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require 'pathname'
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module Circola
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#from any Bio::FlatFile or object iterates through the entries and writes a file in
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6
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#Circos' karyotype format.
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#
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8
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#opts:
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#:id => array of [string method, arg1, arg2, ... ] to apply to entry_id of Bio::Flatfile entry for Circos id column
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#:label => array of [string method, arg1, arg2, ... ] to apply to entry_id of Bio::Flatfile entry for Circos id column
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11
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#:color => array of color strings for Circos color column. Used in order, looped round if too few provided
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#:file => name of file to write to, Defaults to STDOUT if absent or false.
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# returns a File object if written to file
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def each_to_karyotype(opts)
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opts = {
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:id => [:gsub, //,""],
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:label => [:gsub, //,""],
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:colors => ['red', 'green', 'blue', 'purple', 'orange'],
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:file => nil
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}.merge!(opts)
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#raise TypeError "not a Bio::Flatfile" unless self.is_a?(Bio::FlatFile)
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self.must_be Bio::FlatFile
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file = File.open(opts[:file], "w")
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self.each_with_index do |entry, index|
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id = entry.entry_id.send( *opts[:id] )
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27
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label = entry.entry_id.send( *opts[:label] )
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color = Circola.pick_color(opts, index)#opts[:colors][offset]
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file.puts "chr - #{id} #{label} 0 #{entry.length} #{color}"
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end
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file.close
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file
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end
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35
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#assumes text file has id\tlength
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def text_to_karyotype(opts)
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opts = {
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:id => [:gsub, //,""],
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:label => [:gsub, //,""],
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:colors => ['red', 'green', 'blue', 'purple', 'orange'],
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:file => nil
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}.merge!(opts)
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self.must_be File
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file = File.open(opts[:file], "w")
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self.each_with_index do |line, index|
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color = Circola.pick_color(opts, index)
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47
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id,stop = line.chomp.split(/\t/)
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48
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label = id
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49
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id = id.send( *opts[:id] )
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label = label.send( *opts[:label] )
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file.puts "chr - #{id} #{label} 0 #{stop} #{color}"
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end
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file.close
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file
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end
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#gets an array of colour tags from circos conf file, eg. colors.brewer.conf
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59
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def Circola.pick_color(opts, index)
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offset = index - ((opts[:colors].length) * (index / opts[:colors].length) )
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opts[:colors][offset]
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end
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def get_color_list
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self.must_be File
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colors = []
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self.each do |line|
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next if line =~ /^[<#\s]/
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colors << line.split(/\s/)[0]
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end
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colors
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end
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def must_be type
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begin
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raise "not a #{type}" unless self.is_a?(type)
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rescue Exception => e
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$stderr.puts e.backtrace
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end
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end
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#gives the full path of a File object
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def full_path
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must_be File
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File.realpath(self.path)
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end
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#gives relative path from working dir to file
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def relative_path
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must_be File
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Pathname.new(self.full_path).relative_path_from(Pathname.new(Dir.pwd)).to_s
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end
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def Circola.make_ideogram(opts)
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opts = {
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:file => nil,
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:default => "2u",
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:pairwise => nil
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}.merge!(opts)
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f = File.open(opts[:file], "w")
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f.puts "<ideogram>\n<spacing>\n#default = {opts[:default]}\n</spacing></ideogram>"
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f.close
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f
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end
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def Circola.prep_conf(opts)
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opts = {
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:file => nil,
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:chromosomes_units => 1000000,
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:chromosomes_display_default => "yes",
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:karyotype => nil,
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:includes => []
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}.merge!(opts)
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f = File.open(opts[:file], "w")
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[:karyotype, :chromosomes_units, :chromosomes_display_default].each do |par|
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f.puts "#{par} = #{opts[par]}"
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end
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opts[:includes].each do |inc|
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f.puts "<<include #{inc}>>"
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end
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f.close
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f
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end
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125
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def Circola.run_circos(opts)
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opts = {
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:circos => nil,
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:conf => nil
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}.merge!(opts)
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command = "#{opts[:circos]} -conf #{opts[:conf]}"
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$stderr.puts "executing ... #{command}"
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Kernel.exec(command)
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end
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def Circola.clean_up(files)
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files.each{|f| File.delete f }
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end
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138
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end
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140
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141
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: barmcakes
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version: !ruby/object:Gem::Version
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4
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-
version: 0.0.
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4
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version: 0.0.11
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5
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prerelease:
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6
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platform: ruby
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7
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authors:
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@@ -21,6 +21,8 @@ files:
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21
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- lib/barmcakes.rb
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22
22
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- lib/arrghs.rb
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23
23
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- lib/file.rb
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24
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- lib/circola.rb
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25
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- lib/bio_tools.rb
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homepage: http://github.com/danmaclean/barmcakes
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licenses: []
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post_install_message:
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