Class: Bio::GFF::Record

Inherits:
Object show all
Defined in:
lib/bio/db/gff.rb

Overview

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

Direct Known Subclasses

GFF2::Record

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str) ⇒ Record

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


125
126
127
128
129
130
131
# File 'lib/bio/db/gff.rb', line 125

def initialize(str)
  @comment = str.chomp[/#.*/]
  return if /^#/.match(str)
  @seqname, @source, @feature, @start, @end, @score, @strand, @frame,
    attributes, = str.chomp.split("\t")
  @attributes = parse_attributes(attributes) if attributes
end

Instance Attribute Details

#attributesObject

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


103
104
105
# File 'lib/bio/db/gff.rb', line 103

def attributes
  @attributes
end

#commentObject

Comments for the GFF record


106
107
108
# File 'lib/bio/db/gff.rb', line 106

def comment
  @comment
end

#endObject

End position of feature on reference sequence


91
92
93
# File 'lib/bio/db/gff.rb', line 91

def end
  @end
end

#featureObject

Name of the feature


85
86
87
# File 'lib/bio/db/gff.rb', line 85

def feature
  @feature
end

#frameObject

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


100
101
102
# File 'lib/bio/db/gff.rb', line 100

def frame
  @frame
end

#scoreObject

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


94
95
96
# File 'lib/bio/db/gff.rb', line 94

def score
  @score
end

#seqnameObject

Name of the reference sequence


79
80
81
# File 'lib/bio/db/gff.rb', line 79

def seqname
  @seqname
end

#sourceObject

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


82
83
84
# File 'lib/bio/db/gff.rb', line 82

def source
  @source
end

#startObject

Start position of feature on reference sequence


88
89
90
# File 'lib/bio/db/gff.rb', line 88

def start
  @start
end

#strandObject

Strand that feature is located on


97
98
99
# File 'lib/bio/db/gff.rb', line 97

def strand
  @strand
end

Instance Method Details

#commentsObject

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


109
110
111
112
# File 'lib/bio/db/gff.rb', line 109

def comments
  #warn "#{self.class.to_s}#comments is deprecated. Instead, use \"comment\"." if $VERBOSE
  self.comment
end

#comments=(str) ⇒ Object

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


115
116
117
118
# File 'lib/bio/db/gff.rb', line 115

def comments=(str)
  #warn "#{self.class.to_s}#comments= is deprecated. Instead, use \"comment=\"." if $VERBOSE
  self.comment = str
end