Class: Bio::Grid

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/grid.rb,
lib/bio/grid/job.rb

Defined Under Namespace

Classes: Job

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(input, number, uuid) ⇒ Grid 



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# File 'lib/bio/grid.rb', line 6

def initialize(input,number, uuid)
  @input = input
  @number = number
  @uuid = uuid ? uuid : UUID.new.generate.split("-").first 
end

Instance Attribute Details

#input ⇒ Object

Returns the value of attribute input.



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# File 'lib/bio/grid.rb', line 5

def input
  @input
end

#number ⇒ Object

Returns the value of attribute number.



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# File 'lib/bio/grid.rb', line 5

def number
  @number
end

#uuid ⇒ Object

Returns the value of attribute uuid.



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# File 'lib/bio/grid.rb', line 5

def uuid
  @uuid
end

Class Method Details

.run(options) ⇒ Object 



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# File 'lib/bio/grid.rb', line 12

def self.run(options)
  options[:number] = "all" unless options[:number]
  grid = self.new options[:input], options[:number], options[:uuid]
  options[:uuid] = grid.uuid unless options[:uuid]
  groups = grid.prepare_input_groups
  inputs = groups.keys.sort
  groups[inputs.shift].each_with_index do |input1,index|
    if options[:cmd]=~/<(\d+),(\d+)(,\d+)*>/
      step = ($3) ? $3.tr(",","").to_i : 1
      range = Range.new($1.to_i,$2.to_i,false).step(step).to_a
      range.each do |value|
        cmd_line = options[:cmd].gsub(/<(\d+),(\d+)(,\d+)*>/,value.to_s)
        job = Bio::Grid::Job.new(options) # inherit global options
        job.options[:parameter_value] = "-param:#{value}"
        job.execute(cmd_line,inputs,input1,groups,index)
      end
    elsif options[:params]
      options[:params].each do |p|
        cmd_line = options[:cmd].gsub(/<param>|<parameter>/,p)
        job = Bio::Grid::Job.new(options)
        job.options[:parameter_value] = "-param:#{p}"
        job.execute(cmd_line,inputs,input1,groups,index)
      end
    else
      job = Bio::Grid::Job.new(options) # inherit global options
      job.execute(options[:cmd],inputs,input1,groups,index)
    end

    break if options[:test]
  end      
end

Instance Method Details

#prepare_input_groups ⇒ Object 



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# File 'lib/bio/grid.rb', line 44

def prepare_input_groups
  groups = Hash.new {|h,k| h[k] = [] }
  self.input.each_with_index do |location,index|
    list = Dir.glob(location).sort
    raise ArgumentError,"Input file or folder #{location} do not exist!" if list.empty?
    if self.number == "all"
      groups["input#{index+1}"] = [list]
    else
      list.each_slice(self.number.to_i) {|subgroup| groups["input#{index+1}"] << subgroup}
    end
  end
  groups
end