Class: BioDSL::SplitValues

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

Overview

Split the values of a key into new key/value pairs.

split_values splits the value of a given key into multiple values that are added to the record. The keys used for the values are per default based on the given key with an added index, but using the keys option allows specifying a list of keys to use instead.

Usage

split_values(<key>: <string>>[, delimiter: <string>[, keys: <list>]])

Options

# key: <string> - Key who’s value to split.

  • keys: <list> - List of keys to use with split values.

  • delimiter: <string> - Delimiter (default=‘_’).

Examples

Consider the following records:

{ID: "FOO:count=10", SEQ: "gataag"}
{ID: "FOO_10_20", SEQ: "gataag"}

To split the value belinging to ID do:

split_values(key: :ID)

{:ID=>"FOO:count=10", :SEQ=>"gataag"}
{:ID=>"FOO_10_20", :SEQ=>"gataag", :ID_0=>"FOO", :ID_1=>10, :ID_2=>20}

Using a different delimiter:

split_values(key: "ID", delimiter: ':count=')

{:ID=>"FOO:count=10", :SEQ=>"gataag", :ID_0=>"FOO", :ID_1=>10}
{:ID=>"FOO_10_20", :SEQ=>"gataag"}

Using a different delimiter and a list of keys:

split_values(key: "ID", keys: ["ID", :COUNT], delimiter: ':count=')

{:ID=>"FOO", :SEQ=>"gataag", :COUNT=>10}
{:ID=>"FOO_10_20", :SEQ=>"gataag"}

Constant Summary collapse

STATS = 
i(records_in records_out)

Instance Method Summary collapse

Constructor Details

#initialize(options) ⇒ SplitValues

Constructor for SplitValues.

Parameters:

  • options (Hash) —

    Options hash.

Options Hash (options):



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# File 'lib/BioDSL/commands/split_values.rb', line 84

def initialize(options)
  @options = options

  check_options

  @first       = true
  @convert     = []
  @keys        = @options[:keys]
  @key         = @options[:key].to_sym
  @delimiter   = @options[:delimiter] || '_'
end

Instance Method Details

#lmb ⇒ Proc

Return command lambda for split_values.

Returns:

  • (Proc) —

    Command lambda.



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# File 'lib/BioDSL/commands/split_values.rb', line 99

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

    input.each do |record|
      @status[:records_in] += 1

      if (value = record[@key])
        values = value.split(@delimiter)

        if values.size > 1
          determine_types(values) if @first

          split_values(values, record)
        end
      end

      output << record

      @status[:records_out] += 1
    end
  end
end