Class: BioInterchange::Genomics::GFF3Feature

Inherits:
Object
  • Object
show all
Defined in:
lib/biointerchange/genomics/gff3_feature.rb

Overview

Represents a single genomic feature of a GFF3 file.

Direct Known Subclasses

GVFFeature, VCFFeature

Constant Summary collapse

NOT_STRANDED =

Constants determining the strand of the feature.

0
UNKNOWN = 
1
POSITIVE = 
2
NEGATIVE = 
3

Instance Method Summary collapse

Constructor Details

#initialize(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, phase = nil, attributes = {}) ⇒ GFF3Feature

Creates a new feature representation. A feature is described on one line of the GFF3 file.

sequence_id

an identifier that determines the coordinate system for the feature

source

a text description of the origin of this feature description

type

either a SOFA accession, SOFA term, or textual description (the former are URIs, the latter is a string)

start_coordinate

an integer denoting the start coordinate of the feature

end_coordinate

an integer denoting the end coordinate of the feature, which is equal or larger than the start coordinate

score

a floating point score

strand

a constant determining whether the feature is NOT_STRANDED, the strand is UNKNOWN, or the feature is on the POSITIVE or NEGATIVE strand

phase

an integer determining the phase of the feature, if the feature has a phase

attributes

a map of additional attributes associated with the feature



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 23

def initialize(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, phase = nil, attributes = {})
  @sequence_id = sequence_id
  @source = source
  @type = type
  @start_coordinate = start_coordinate
  @end_coordinate = end_coordinate
  @score = score
  @strand = strand
  @phase = phase
  @attributes = attributes
end

Instance Method Details

#attributes ⇒ Object

Returns a map of additional attributes for this feature.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 76

def attributes
  @attributes.freeze
end

#end_coordinate ⇒ Object

Returns the end coordinate of the feature. The end coordinate is equal or larger than the start coordinate.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 56

def end_coordinate
  @end_coordinate
end

#phase ⇒ Object

Returns the phase, if existing, for this feature.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 71

def phase
  @phase
end

#score ⇒ Object

Returns the score of the feature. The score is a floating point number, which ideally is an E-value or P-value.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 61

def score
  @score
end

#sequence_id ⇒ Object

Returns the sequence ID that determines the coordinate system for the feature.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 36

def sequence_id
  @sequence_id
end

#source ⇒ Object

Returns a textual description that determines the origin of this feature.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 41

def source
  @source
end

#start_coordinate ⇒ Object

Returns the start coordinate of the feature. The start coordinate is equal or smaller than the end coordinate.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 51

def start_coordinate
  @start_coordinate
end

#strand ⇒ Object

Returns the strand the feature is located on.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 66

def strand
  @strand
end

#type ⇒ Object

Returns the feature type, which can either be a SOFA URI or a textual description otherwise.



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# File 'lib/biointerchange/genomics/gff3_feature.rb', line 46

def type
  @type
end