class Bio::GFF::GFF3::Record

Represents a single line of a GFF3-formatted file. See Bio::GFF::GFF3 for more information.

Public Class Methods

Source

     # File lib/bio/db/gff.rb
1165 def initialize(*arg)
1166   super(*arg)
1167 end

Creates a Bio::GFF::GFF3::Record object. Is typically not called directly, but is called automatically when creating a Bio::GFF::GFF3 object.

Arguments:

str: a tab-delimited line in GFF3 format

Arguments:

seqid: sequence ID (String or nil)
source: source (String or nil)
feature_type: type of feature (String)
start_position: start (Integer)
end_position: end (Integer)
score: score (Float or nil)
strand: strand (String or nil)
phase: phase (Integer or nil)
attributes: attributes (Array or nil)

Calls superclass method Bio::GFF::GFF2::Record::new

parse (str)

Source

     # File lib/bio/db/gff.rb
1144 def self.parse(str)
1145   self.new.parse(str)
1146 end

Parses a GFF3-formatted line and returns a new Bio::GFF::GFF3::Record object.

Public Instance Methods

id ()

Source

     # File lib/bio/db/gff.rb
1118 def id
1119   get_attribute('ID')
1120 end

shortcut to the ID attribute

id= (str)

Source

     # File lib/bio/db/gff.rb
1123 def id=(str)
1124   set_attribute('ID', str)
1125 end

set ID attribute

parse (string)

Source

     # File lib/bio/db/gff.rb
1171 def parse(string)
1172   super
1173 end

Parses a GFF3-formatted line and stores data from the string. Note that all existing data is wiped out.

Calls superclass method Bio::GFF::GFF2::Record::parse

to_s ()

Source

     # File lib/bio/db/gff.rb
1176 def to_s
1177   cmnt = if defined?(@comment) and @comment and
1178              !@comment.to_s.strip.empty? then
1179            @comment.gsub(/[\r\n]+/, ' ')
1180          else
1181            false
1182          end
1183   return "\##{cmnt}\n" if self.comment_only? and cmnt
1184   [
1185    escape_seqid(column_to_s(@seqname)),
1186    escape(column_to_s(@source)),
1187    escape(column_to_s(@feature)),
1188    escape(column_to_s(@start)),
1189    escape(column_to_s(@end)),
1190    escape(column_to_s(@score)),
1191    escape(column_to_s(@strand)),
1192    escape(column_to_s(@frame)),
1193    attributes_to_s(@attributes)
1194   ].join("\t") + 
1195     (cmnt ? "\t\##{cmnt}\n" : "\n")
1196 end

Return the record as a GFF3 compatible string