class Bio::GFF::GFF2

DESCRIPTION ↑

Represents version 2 of GFF specification. Its behavior is somehow different from Bio::GFF, especially for attributes.

Constants

VERSION

Attributes

gff_version[R]

GFF2 version string (String or nil). nil means “2”.

metadata[RW]

Metadata (except “##gff-version”). Must be an array of Bio::GFF::GFF2::MetaData objects.

Public Class Methods

new(str = nil) click to toggle source

Creates a Bio::GFF::GFF2 object by building a collection of Bio::GFF::GFF2::Record (and metadata) objects.

Arguments:

  • str: string in GFF format

Returns

Bio::GFF::GFF2 object

    # File lib/bio/db/gff.rb
825 def initialize(str = nil)
826   @gff_version = nil
827   @records = []
828   @metadata = []
829   parse(str) if str
830 end

Public Instance Methods

parse(str) click to toggle source

Parses a GFF2 entries, and concatenated the parsed data.

Arguments:

  • str: string in GFF format

Returns

self

    # File lib/bio/db/gff.rb
845 def parse(str)
846   # parses GFF lines
847   str.each_line do |line|
848     if /^\#\#([^\s]+)/ =~ line then
849       parse_metadata($1, line)
850     else
851       @records << GFF2::Record.new(line)
852     end
853   end
854   self
855 end
to_s() click to toggle source

string representation of the whole entry.

    # File lib/bio/db/gff.rb
194 def to_s
195   ver = @gff_version || VERSION.to_s
196   ver = ver.gsub(/[\r\n]+/, ' ')
197   ([ "##gff-version #{ver}\n" ] +
198    @metadata.collect { |m| m.to_s } +
199    @records.collect{ |r| r.to_s }).join('')
200 end