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

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

Methods

comments   comments=   new  

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)

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

[Source]

     # File lib/bio/db/gff.rb, line 125
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()

"comments" is deprecated. Instead, use "comment".

[Source]

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

"comments=" is deprecated. Instead, use "comment=".

[Source]

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

[Validate]