Method: BioTable::TableApply#initialize

Defined in:
lib/bio-table/table_apply.rb

#initialize(options) ⇒ TableApply

Returns a new instance of TableApply.



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# File 'lib/bio-table/table_apply.rb', line 10

def initialize options
  @logger = Bio::Log::LoggerPlus['bio-table']

  # @skip  = options[:skip]
  # @logger.debug "Skipping #{@skip} lines" if @skip
  @num_filter  = options[:num_filter]
  @logger.debug "Filtering on #{@num_filter}" if @num_filter 
  @filter  = options[:filter]
  @logger.debug "Filtering on #{@filter}" if @filter 
  @rewrite  = options[:rewrite]
  @logger.debug "Rewrite #{@rewrite}" if @rewrite
  @use_columns = options[:columns]
  @logger.debug "Filtering on columns #{@use_columns}" if @use_columns 
  @column_filter = options[:column_filter]
  @logger.debug "Filtering on column names #{@column_filter}" if @column_filter
  @strip_quotes = options[:strip_quotes]
  @logger.debug "Strip quotes #{@strip_quotes}" if @strip_quotes
  @transform_ids = options[:transform_ids]
  @logger.debug "Transform ids #{@transform_ids}" if @transform_ids
  @include_rownames = options[:with_rownames]
  @logger.debug "Include row names" if @include_rownames
  @first_column = (@include_rownames ? 0 : 1)
  @write_header = options[:write_header]
end