Class: Bio::Krona

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-krona/krona.rb

Class Method Summary collapse

Class Method Details

.collapse(count_hash, max_level) ⇒ Object

Take a count_hash (hash of Array => Numeric), and collapse the array down to some maximum number of levels. In krona, the collapsed output would now have less (max_level) rings.

Returns the collapsed count_hash



77
78
79
80
81
82
83
84
85
86
87
88
 
# File 'lib/bio-krona/krona.rb', line 77

def self.collapse(count_hash, max_level)
  raise unless max_level.kind_of?(Integer) and max_level > 0
  new_count_hash = {}
  count_hash.each do |array, count|
    raise unless array.kind_of?(Array)
    raise unless count.kind_of?(Numeric)

    new_count_hash[array[0...max_level]] ||= 0
    new_count_hash[array[0...max_level]] += count
  end
  return new_count_hash
end

.html(count_hash, options = {}) ⇒ Object

Given a count_hash, return the html generated by krona

  • count_hash: hash of Array => Numeric, where the array is a list of descriptors (e.g. [Eukaryota, Metazoa, Chordata]), and the Numeric is a count for the number of observations of that description

  • options:

** :krona_path: path to the ktImportText script in the krona directory (default ‘ktImportText’ i.e. assuming it is already in the PATH) ** :resources_url: URL of krona resources (i.e. the -u option of ktImportText) ** :multiple_samples: count_hash is a hash of sample names to hash of Array => Numeric, when multiple samples are to be included [default false]



12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
 
# File 'lib/bio-krona/krona.rb', line 12

def self.html(count_hash, options={})
  raise unless count_hash.kind_of?(Hash)
  options[:krona_path] ||= %(ktImportText)

  get_tempfile_from_count_hash = lambda do |ch|
    tempfile = Tempfile.new('krona')
    ch.each do |array, count|
      raise unless array.kind_of?(Array)
      raise unless count.kind_of?(Numeric)

      tempfile.puts [
        count,
        array
      ].flatten.join("\t")
    end
    tempfile.close
    tempfile
  end

  input_tempfiles = []
  input_names = []
  if options[:multiple_samples]
    input_names = count_hash.keys
    input_tempfiles = count_hash.values.collect{|ch| get_tempfile_from_count_hash.call(ch)}
  else
    input_names = [nil]
    input_tempfiles = [get_tempfile_from_count_hash.call(count_hash)]
  end

  pairs = []
  input_names.each_with_index do |name, i|
    tmpname = input_tempfiles[i].path
    if name.nil?
      pairs.push tmpname
    else
      pairs.push "#{tmpname},#{name}"
    end
  end

  Tempfile.open('krona_out') do |output|
    output.close

    command = [
      options[:krona_path],
      '-o',
      output.path,
      pairs,
      ].flatten
    if options[:resources_url]
      command.push '-u'
      command.push options[:resources_url]
    end
    Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
      err = stderr.read
      raise err unless err==''
    end

    input_tempfiles.each{|t| t.close}
    return File.open(output.path).read
  end
end