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
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” 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=” 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