class BioInterchange::Genomics::GVFReader
Public Class Methods
new(name = nil, name_uri = nil, date = nil, batch_size = nil)
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Creates a new instance of a Genome Variation Format (GVF) reader.
name
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Optional name of the person who generated the GVF file.
name_uri
-
Optional e-mail address of the person who generated the GVF file.
date
-
Optional date of when the GVF file was produced.
Calls superclass method
BioInterchange::Genomics::GFF3Reader::new
# File lib/biointerchange/genomics/gvf_reader.rb, line 24 def initialize(name = nil, name_uri = nil, date = nil, batch_size = nil) # Remember: calling super without brackets passes all arguments of initialize! super end
Protected Instance Methods
add_pragma(feature_set, line)
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Calls superclass method
BioInterchange::Genomics::GFF3Reader#add_pragma
# File lib/biointerchange/genomics/gvf_reader.rb, line 35 def add_pragma(feature_set, line) line.chomp! name, value = line[2..-1].split(/\s/, 2) value.strip! if value # Interpret pragmas, and if not known, delegate to GFF3Reader (in alphabetical order): if name == 'attribute-method' or name == 'data-source' or name == 'score-method' or name == 'source-method' or name == 'technology-platform' then attributes = split_attributes(value) structured_attributes = feature_set.pragma(name) structured_attributes = { name => [] } unless structured_attributes structured_attributes[name] << attributes feature_set.set_pragma(name, structured_attributes) elsif name == 'gvf-version' then feature_set.set_pragma(name, { name => value.to_f }) else super(feature_set, line) end end
create_feature_set()
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# File lib/biointerchange/genomics/gvf_reader.rb, line 31 def create_feature_set BioInterchange::Genomics::GVFFeatureSet.new() end