class BioTable::TableApply
Apply filters/rewrite etc. to a table, visiting a row at a time. For optimization this class contains some state
Attributes
first_column[R]
Public Class Methods
new(options)
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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
Public Instance Methods
column_index(header)
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# File lib/bio-table/table_apply.rb, line 47 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)
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# File lib/bio-table/table_apply.rb, line 35 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 and @write_header header end
parse_row(line_num, line, header, column_idx, prev_fields, options)
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Take a line as a string and return it as a tuple of rowname and datafields
# File lib/bio-table/table_apply.rb, line 55 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 == [] if options[:pad_fields] and fields.size < header.size fields += [''] * (header.size - fields.size) end 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