Class: Bio::GFF::Record

Inherits:

Object

• Object
• Bio::GFF::Record

show all

Defined in:

lib/bio/db/gff.rb

Overview

Instance Attribute Summary (collapse)

• - (Object) attributes

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

• - (Object) comment

  Comments for the GFF record.

• - (Object) end

  End position of feature on reference sequence.

• - (Object) feature

  Name of the feature.

• - (Object) frame

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

• - (Object) score

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

• - (Object) seqname

  Name of the reference sequence.

• - (Object) source

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

• - (Object) start

  Start position of feature on reference sequence.

• - (Object) strand

  Strand that feature is located on.

Instance Method Summary (collapse)

• - (Object) comments

  "comments" is deprecated.

• - (Object) comments=(str)

  "comments=" is deprecated.

• - (Record) initialize(str) constructor

  Creates a Bio::GFF::Record object.

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# 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

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

def attributes
  @attributes
end

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

def comment
  @comment
end

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

def end
  @end
end

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

def feature
  @feature
end

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

def frame
  @frame
end

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

def score
  @score
end

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

def seqname
  @seqname
end

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

def source
  @source
end

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

def start
  @start
end

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

def strand
  @strand
end

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# 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

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# 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