Method: Bio::Blast.reports_xml

Defined in:

lib/bio/appl/blast.rb

.reports_xml(input, parser = nil) ⇒ Object

Note that this is the old implementation of Bio::Blast.reports. The aim of this method is keeping compatibility for older BLAST XML documents which might not be parsed by the new Bio::Blast.reports nor Bio::FlatFile. (Though we are not sure whether such documents exist or not.)

Bio::Blast.reports_xml parses given data, and returns an array of Bio::Blast::Report objects, or yields each Bio::Blast::Report object when a block is given.

It can be used only for XML format. For default (-m 0) format, consider using Bio::FlatFile, or Bio::Blast.reports.

---

Arguments:

• input (required): input data

• parser: type of parser. see Bio::Blast::Report.new

Returns

Undefiend when a block is given. Otherwise, an Array containing Bio::Blast::Report objects.

# File 'lib/bio/appl/blast.rb', line 220

def self.reports_xml(input, parser = nil)
  ary = []
  input.each_line("</BlastOutput>\n") do |xml|
    xml.sub!(/[^<]*(<?)/, '\1') # skip before <?xml> tag
    next if xml.empty?          # skip trailing no hits
    rep = Report.new(xml, parser)
    if rep.reports then
      if block_given?
        rep.reports.each { |r| yield r }
      else
        ary.concat rep.reports
      end
    else
      if block_given?
        yield rep
      else
        ary.push rep
      end
    end
  end
  return ary
end