Class: MiGA::Taxonomy

Inherits:
MiGA
  • Object
show all
Includes:
Base
Defined in:
lib/miga/taxonomy.rb,
lib/miga/taxonomy/base.rb

Defined Under Namespace

Modules: Base

Constant Summary

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from Common::Path

#root_path, #script_path

Methods included from Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from Common::Net

#download_file_ftp, #known_hosts, #remote_connection

Methods included from Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

#initialize(str, ranks = nil, alt = []) ⇒ Taxonomy

Create MiGA::Taxonomy from String or Array str. The string is a series of space-delimited entries, the array is a vector of entries. Each entry can be either a rank:value pair (if ranks is nil), or just values in the same order as ther ranks in ranks. Alternatively, str as a Hash with rank => value pairs is also supported. If alt is passed, it must be an Array of String, Array, or Hash entries as defined above (except ranks are not allowed).



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# File 'lib/miga/taxonomy.rb', line 23

def initialize(str, ranks = nil, alt = [])
  reset(str, ranks)
  @alt = (alt || []).map { |i| Taxonomy.new(i) }
end

Instance Attribute Details

#ranks ⇒ Object (readonly)

Taxonomic hierarchy Hash.



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# File 'lib/miga/taxonomy.rb', line 13

def ranks
  @ranks
end

Class Method Details

.json_create(o) ⇒ Object

Initialize from JSON-derived Hash o



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# File 'lib/miga/taxonomy/base.rb', line 23

def json_create(o)
  new(o['str'], nil, o['alt'])
end

.KNOWN_RANKS ⇒ Object 



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# File 'lib/miga/taxonomy/base.rb', line 27

def KNOWN_RANKS()
  @@KNOWN_RANKS
end

.LONG_RANKS ⇒ Object 



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# File 'lib/miga/taxonomy/base.rb', line 31

def LONG_RANKS()
  @@LONG_RANKS
end

.normalize_rank(rank) ⇒ Object

Returns cannonical rank (Symbol) for the rank String



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# File 'lib/miga/taxonomy/base.rb', line 8

def normalize_rank(rank)
  return rank.to_sym if @@_KNOWN_RANKS_H[rank.to_sym]

  rank = rank.to_s.downcase
  return nil if rank == 'no rank'

  rank = @@RANK_SYNONYMS[rank] unless @@RANK_SYNONYMS[rank].nil?
  rank = rank.to_sym
  return nil unless @@_KNOWN_RANKS_H[rank]

  rank
end

Instance Method Details

#<<(value) ⇒ Object

Add value to the hierarchy, that can be an Array, a String, or a Hash, as described in #initialize.



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# File 'lib/miga/taxonomy.rb', line 43

def <<(value)
  case value
  when Hash
    value.each do |r, n|
      next if n.nil? || n == ''

      @ranks[self.class.normalize_rank(r)] = n.tr('_', ' ')
    end
  when Array
    value.each { |v| self << v }
  when String
    self << Hash[*value.split(':', 2)]
  else
    raise 'Unsupported class: ' + value.class.name
  end
end

#[](rank) ⇒ Object Also known as: fetch

Get rank value.



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# File 'lib/miga/taxonomy.rb', line 62

def [](rank)
  @ranks[rank.to_sym]
end

#add_alternative(tax, replace = true) ⇒ Object

Add an alternative taxonomy. If the namespace matches an existing namespace, the alternative (or master) is replaced instead if replace is true.



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# File 'lib/miga/taxonomy.rb', line 91

def add_alternative(tax, replace = true)
  raise 'Unsupported taxonomy class.' unless tax.is_a? MiGA::Taxonomy

  alt_ns = alternative(tax.namespace)
  if !replace || tax.namespace.nil? || alt_ns.nil?
    @alt << tax
  else
    alt_ns.reset(tax.to_s)
  end
end

#alternative(which = nil) ⇒ Object

Get the alternative taxonomies.

  • If which is nil (default), returns all alternative taxonomies as Array (not including the master taxonomy).

  • If which is Integer, returns the indexed taxonomy (starting with 0, the master taxonomy).

  • Otherwise, returns the first taxonomy with namespace which (coerced as String), including the master taxonomy.

In the latter two cases it can be nil.



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# File 'lib/miga/taxonomy.rb', line 77

def alternative(which = nil)
  case which
  when nil
    @alt
  when Integer
    ([self] + @alt)[which]
  else
    ([self] + @alt).find { |i| i.namespace.to_s == which.to_s }
  end
end

#delete_alternative ⇒ Object

Removes (and returns) all alternative taxonomies.



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# File 'lib/miga/taxonomy.rb', line 104

def delete_alternative
  alt = @alt.dup
  @alt = []
  alt
end

#highest(force_ranks = false) ⇒ Object

Get the most general rank as a two-entry Array (rank and value). If force_ranks is true, it always returns the value for domain (d) even if undefined.



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# File 'lib/miga/taxonomy.rb', line 143

def highest(force_ranks = false)
  sorted_ranks(force_ranks).first
end

#in?(taxon) ⇒ Boolean

Evaluates if the loaded taxonomy includes taxon. It assumes that taxon only has one informative rank. The evaluation is case-insensitive.

Returns:

  • (Boolean) 


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# File 'lib/miga/taxonomy.rb', line 113

def in?(taxon)
  r = taxon.ranks.keys.first
  return false if self[r].nil?

  self[r].casecmp(taxon[r]).zero?
end

#lowest(force_ranks = false) ⇒ Object

Get the most specific rank as a two-entry Array (rank and value). If force_ranks is true, it always returns the value for dataset (ds) even if undefined.



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# File 'lib/miga/taxonomy.rb', line 151

def lowest(force_ranks = false)
  sorted_ranks(force_ranks).last
end

#namespace ⇒ Object

Namespace of the taxonomy (a String) or nil.



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# File 'lib/miga/taxonomy.rb', line 135

def namespace
  self[:ns]
end

#reset(str, ranks = nil) ⇒ Object

Reset ranks (including namespace) while leaving alternatives untouched. See #initialize for str and ranks.



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# File 'lib/miga/taxonomy.rb', line 31

def reset(str, ranks = nil)
  @ranks = {}
  if ranks.nil?
    initialize_by_str(str)
  else
    initialize_by_ranks(str, ranks)
  end
end

#sorted_ranks(force_ranks = false, with_namespace = false) ⇒ Object

Sorted list of ranks, as an Array of two-entry Arrays (rank and value). If force_ranks is true, it returns all standard ranks even if undefined. If with_namespace is true, it includes also the namespace.



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# File 'lib/miga/taxonomy.rb', line 124

def sorted_ranks(force_ranks = false, with_namespace = false)
  @@KNOWN_RANKS.map do |r|
    next if
      (r == :ns && !with_namespace) || (ranks[r].nil? && !force_ranks)

    [r, ranks[r]]
  end.compact
end

#to_json(*a) ⇒ Object

Generate JSON-formated String representing the taxonomy.



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# File 'lib/miga/taxonomy.rb', line 165

def to_json(*a)
  hsh = { JSON.create_id => self.class.name, 'str' => to_s }
  hsh['alt'] = alternative.map(&:to_s) unless alternative.empty?
  hsh.to_json(*a)
end

#to_s(force_ranks = false) ⇒ Object

Generate cannonical String for the taxonomy. If force_ranks is true, it returns all the standard ranks even if undefined.



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# File 'lib/miga/taxonomy.rb', line 158

def to_s(force_ranks = false)
  sorted_ranks(force_ranks, true)
    .map { |r| "#{r[0]}:#{(r[1] || '').gsub(/[\s:]/, '_')}" }.join(' ')
end