Method: Bio::GFF::GFF3#parse

Defined in:
lib/bio/db/gff.rb

#parse(str) ⇒ Object

Parses a GFF3 entries, and concatenated the parsed data.

Note that after “##FASTA” line is given, only fasta-formatted text is accepted.

Arguments:

  • str: string in GFF format

Returns

self



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# File 'lib/bio/db/gff.rb', line 912

def parse(str)
  # if already after the ##FASTA line, parses fasta format and return
  if @in_fasta then
    parse_fasta(str)
    return self
  end

  if str.respond_to?(:gets) then
    # str is a IO-like object
    fst = nil
  else
    # str is a String
    gff, sep, fst = str.split(/^(\>|##FASTA.*)/n, 2)
    fst = sep + fst if sep == '>' and fst
    str = gff
  end

  # parses GFF lines
  str.each_line do |line|
    if /^\#\#([^\s]+)/ =~ line then
      parse_metadata($1, line)
      parse_fasta(str) if @in_fasta
    elsif /^\>/ =~ line then
      @in_fasta = true
      parse_fasta(str, line)
    else
      @records << GFF3::Record.new(line)
    end
  end

  # parses fasta format when str is a String and fasta data exists
  if fst then
    @in_fasta = true
    parse_fasta(fst)
  end

  self
end