Class Bio::GFF::GFF3::Record
In: lib/bio/db/gff.rb
Parent: GFF2::Record

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

Methods

id   id=   new   parse   parse   to_s  

Included Modules

GFF3::Escape

Classes and Modules

Class Bio::GFF::GFF3::Record::Gap
Class Bio::GFF::GFF3::Record::Target

External Aliases

seqname -> seqid
  aliases for Column 1 (formerly "seqname")
seqname= -> seqid=
feature -> feature_type
  aliases for Column 3 (formerly "feature"). In the GFF3 document song.sourceforge.net/gff3.shtml, column3 is called "type", but we used "feature_type" because "type" is already used by Ruby itself.
feature= -> feature_type=
frame -> phase
  aliases for Column 8
frame= -> phase=

Public Class methods

new(*arg)

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)

[Source]

      # File lib/bio/db/gff.rb, line 1130
1130:         def initialize(*arg)
1131:           super(*arg)
1132:         end
parse(str)

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

[Source]

      # File lib/bio/db/gff.rb, line 1109
1109:         def self.parse(str)
1110:           self.new.parse(str)
1111:         end

Public Instance methods

id()

shortcut to the ID attribute

[Source]

      # File lib/bio/db/gff.rb, line 1083
1083:         def id
1084:           get_attribute('ID')
1085:         end
id=(str)

set ID attribute

[Source]

      # File lib/bio/db/gff.rb, line 1088
1088:         def id=(str)
1089:           set_attribute('ID', str)
1090:         end
parse(string)

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

[Source]

      # File lib/bio/db/gff.rb, line 1136
1136:         def parse(string)
1137:           super
1138:         end
to_s()

Return the record as a GFF3 compatible string

[Source]

      # File lib/bio/db/gff.rb, line 1141
1141:         def to_s
1142:           cmnt = if @comment and !@comment.to_s.strip.empty? then
1143:                    @comment.gsub(/[\r\n]+/, ' ')
1144:                  else
1145:                    false
1146:                  end
1147:           return "\##{cmnt}\n" if self.comment_only? and cmnt
1148:           [
1149:            escape_seqid(column_to_s(@seqname)),
1150:            escape(column_to_s(@source)),
1151:            escape(column_to_s(@feature)),
1152:            escape(column_to_s(@start)),
1153:            escape(column_to_s(@end)),
1154:            escape(column_to_s(@score)),
1155:            escape(column_to_s(@strand)),
1156:            escape(column_to_s(@frame)),
1157:            attributes_to_s(@attributes)
1158:           ].join("\t") + 
1159:             (cmnt ? "\t\##{cmnt}\n" : "\n")
1160:         end

[Validate]