class BioInterchange::Genomics::GVFFeature

Represents a single genomic feature of a GVF file.

Public Class Methods

new(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, attributes = {}) click to toggle source

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

attributes

a map of additional attributes associated with the feature

# File lib/biointerchange/genomics/gvf_feature.rb, line 16
def initialize(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, attributes = {})
  # Fill in phase, which is always omitted in GVF features (after 'strand', before 'attributes'):
  super(sequence_id, source, type, start_coordinate, end_coordinate, score, strand, nil, attributes)
end