class Bio::GFF::Record

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

Attributes

attributes[RW]

List of tag=value pairs (e.g. to store name of the feature: ID=my_id)

comment[RW]

Comments for the GFF record

end[RW]

End position of feature on reference sequence

feature[RW]

Name of the feature

frame[RW]

For features of type 'exon': indicates where feature begins in the reading frame

score[RW]

Score of annotation (e.g. e-value for BLAST search)

seqname[RW]

Name of the reference sequence

source[RW]

Name of the source of the feature (e.g. program that did prediction)

start[RW]

Start position of feature on reference sequence

strand[RW]

Strand that feature is located on

Public Class Methods

new(str) click to toggle source

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

Arguments:

str: a tab-delimited line in GFF format

    # File lib/bio/db/gff.rb
125 def initialize(str)
126   @comment = str.chomp[/#.*/]
127   return if /^#/.match(str)
128   @seqname, @source, @feature, @start, @end, @score, @strand, @frame,
129     attributes, = str.chomp.split("\t")
130   @attributes = parse_attributes(attributes) if attributes
131 end

Public Instance Methods

comments() click to toggle source

“comments” is deprecated. Instead, use “comment”.

    # File lib/bio/db/gff.rb
109 def comments
110   #warn "#{self.class.to_s}#comments is deprecated. Instead, use \"comment\"." if $VERBOSE
111   self.comment
112 end

comments=(str) click to toggle source

“comments=” is deprecated. Instead, use “comment=”.

    # File lib/bio/db/gff.rb
115 def comments=(str)
116   #warn "#{self.class.to_s}#comments= is deprecated. Instead, use \"comment=\"." if $VERBOSE
117   self.comment = str
118 end