class Bio::GFF::Record
Represents a single line of a GFF-formatted file. See Bio::GFF for more information.
Attributes
List of tag=value pairs (e.g. to store name of the feature: ID=my_id)
Comments for the GFF record
End position of feature on reference sequence
Name of the feature
For features of type ‘exon’: indicates where feature begins in the reading frame
Score of annotation (e.g. e-value for BLAST search)
Name of the reference sequence
Name of the source of the feature (e.g. program that did prediction)
Start position of feature on reference sequence
Strand that feature is located on
Public Class Methods
Source
# File lib/bio/db/gff.rb 126 def initialize(str) 127 @comment = str.chomp[/#.*/] 128 return if /^#/.match(str) 129 @seqname, @source, @feature, @start, @end, @score, @strand, @frame, 130 attributes, = str.chomp.split("\t") 131 @attributes = parse_attributes(attributes) if attributes 132 end
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
GFFformat
Public Instance Methods
Source
# File lib/bio/db/gff.rb 110 def comments 111 #warn "#{self.class.to_s}#comments is deprecated. Instead, use \"comment\"." if $VERBOSE 112 self.comment 113 end
“comments” is deprecated. Instead, use “comment”.
Source
# File lib/bio/db/gff.rb 116 def comments=(str) 117 #warn "#{self.class.to_s}#comments= is deprecated. Instead, use \"comment=\"." if $VERBOSE 118 self.comment = str 119 end
“comments=” is deprecated. Instead, use “comment=”.