Class: Bio::GFF::GFF2

Inherits:

Bio::GFF

• Object
• Bio::GFF
• Bio::GFF::GFF2

show all

Defined in:

lib/bio/db/gff.rb

Overview

Defined Under Namespace

Modules: Escape Classes: MetaData, Record

Constant Summary

VERSION =

2

Instance Attribute Summary (collapse)

• - (Object) gff_version readonly

  GFF2 version string (String or nil).

• - (Object) metadata

  Metadata (except "##gff-version").

Attributes inherited from Bio::GFF

#records

Instance Method Summary (collapse)

• - (GFF2) initialize(str = nil) constructor

  Creates a Bio::GFF::GFF2 object by building a collection of Bio::GFF::GFF2::Record (and metadata) objects.

• - (Object) parse(str)

  Parses a GFF2 entries, and concatenated the parsed data.

• - (Object) to_s

  string representation of the whole entry.

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# File 'lib/bio/db/gff.rb', line 822

def initialize(str = nil)
  @gff_version = nil
  @records = []
  @metadata = []
  parse(str) if str
end

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# File 'lib/bio/db/gff.rb', line 830

def gff_version
  @gff_version
end

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# File 'lib/bio/db/gff.rb', line 834

def metadata
  @metadata
end

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# File 'lib/bio/db/gff.rb', line 842

def parse(str)
  # parses GFF lines
  str.each_line do |line|
    if /^\#\#([^\s]+)/ =~ line then
      parse_metadata($1, line)
    else
      @records << GFF2::Record.new(line)
    end
  end
  self
end

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# File 'lib/bio/db/gff.rb', line 194

def to_s
  ver = @gff_version || VERSION.to_s
  ver = ver.gsub(/[\r\n]+/, ' ')
  ([ "##gff-version #{ver}\n" ] +
   @metadata.collect { |m| m.to_s } +
   @records.collect{ |r| r.to_s }).join('')
end