Class: BioTable::TableApply

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-table/table_apply.rb

Overview

Apply filters/rewrite etc. to a table, visiting a row at a time. For optimization this class contains some state

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#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)
end

Instance Attribute Details

#first_column ⇒ Object (readonly)

Returns the value of attribute first_column.



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# File 'lib/bio-table/table_apply.rb', line 8

def first_column
  @first_column
end

Instance Method Details

#column_index(header) ⇒ Object 



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# File 'lib/bio-table/table_apply.rb', line 46

def column_index(header)
  column_idx = Filter::create_column_index(@use_columns,header)
  column_idx = Filter::filter_column_index(column_idx,header,@column_filter)
  new_header = Filter::apply_column_filter(header,column_idx)
  return column_idx, new_header
end

#parse_header(line, options) ⇒ Object 



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# File 'lib/bio-table/table_apply.rb', line 34

def parse_header(line, options)  
  header = LineParser::parse(line, options[:in_format], options[:split_on])
  header = Formatter::strip_quotes(header) if @strip_quotes
  # Transform converts the header to upper/lower case
  header = Formatter::transform_header_ids(@transform_ids, header) if @transform_ids
  if options[:unshift_headers]
    header.unshift("ID")
  end
  @logger.info(header) if @logger
  header
end

#parse_row(line_num, line, header, column_idx, prev_fields, options) ⇒ Object 



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# File 'lib/bio-table/table_apply.rb', line 53

def parse_row(line_num, line, header, column_idx, prev_fields, options)
  fields = LineParser::parse(line, options[:in_format], options[:split_on])
  return nil,nil if fields.compact == []
  fields = Formatter::strip_quotes(fields) if @strip_quotes
  fields = Formatter::transform_row_ids(@transform_ids, fields) if @transform_ids
  fields = Filter::apply_column_filter(fields,column_idx) 
  return nil,nil if fields.compact == []
  rowname = fields[0]
  data_fields = fields[@first_column..-1]
  if data_fields.size > 0
    return nil,nil if not Validator::valid_row?(line_num, data_fields, prev_fields)
    return nil,nil if not Filter::numeric(@num_filter,data_fields,header)
    return nil,nil if not Filter::generic(@filter,data_fields,header)
    (rowname, data_fields) = Rewrite::rewrite(@rewrite,rowname,data_fields)
  end
  return rowname, data_fields
end