Class: BioDSL::CountValues

Inherits:
Object
  • Object
show all
Defined in:
lib/BioDSL/commands/count_values.rb

Overview

Count the number of times values of given keys exists in stream.

count_values count the values for a given comma seperated list of keys.

Usage

count_values(<keys: <list>)

Options

  • keys: <list> - Keys whos values to count.

Examples

Consider the following two column table in the file ‘test.tab`:

Human   H1
Human   H2
Human   H3
Dog     D1
Dog     D2
Mouse   M1

To count the values of both columns we first read the table with read_table and then pass the result to count_values:

BD.new.
read_table(input: "test.tab").
count_values(keys: [:V0, :V1]).
dump.
run

{:V0=>"Human", :V1=>"H1", :V0_COUNT=>3, :V1_COUNT=>1}
{:V0=>"Human", :V1=>"H2", :V0_COUNT=>3, :V1_COUNT=>1}
{:V0=>"Human", :V1=>"H3", :V0_COUNT=>3, :V1_COUNT=>1}
{:V0=>"Dog", :V1=>"D1", :V0_COUNT=>2, :V1_COUNT=>1}
{:V0=>"Dog", :V1=>"D2", :V0_COUNT=>2, :V1_COUNT=>1}
{:V0=>"Mouse", :V1=>"M1", :V0_COUNT=>1, :V1_COUNT=>1}

Constant Summary collapse

STATS = 
%i(records_in records_out)

Instance Method Summary collapse

Constructor Details

#initialize(options) ⇒ CountValues

Constructor for CountValues.

Parameters:

  • options (Hash) —

    Options hash.

Options Hash (options):

  • List (Array) —

    of keys whos values to count.



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# File 'lib/BioDSL/commands/count_values.rb', line 76

def initialize(options)
  @options = options

  check_options

  @keys       = @options[:keys].map(&:to_sym)
  @count_hash = Hash.new { |h, k| h[k] = Hash.new(0) }
end

Instance Method Details

#lmb ⇒ Proc

Return the command lambda for the count_values command.

Returns:

  • (Proc) —

    Return command lambda.



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# File 'lib/BioDSL/commands/count_values.rb', line 88

def lmb
  lambda do |input, output, status|
    status_init(status, STATS)

    TmpDir.create('count_values') do |tmp_file, _|
      process_input(input, tmp_file)
      process_output(output, tmp_file)
    end
  end
end