Class: ConvertUtil

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/convert_util.rb

Class Method Summary collapse

Class Method Details

.ensure_mzml_indexed(run_file) ⇒ Object


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# File 'lib/protk/convert_util.rb', line 6

def self.ensure_mzml_indexed(run_file)
  if unindexed_mzml?(run_file)
    index_mzml(run_file)
  end
end

.index_mzml(mzml_file) ⇒ Object


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# File 'lib/protk/convert_util.rb', line 12

def self.index_mzml(mzml_file)
  Dir.mktmpdir do |tmpdir|
    genv=Constants.instance
    %x["#{genv.msconvert} -o #{tmpdir} #{mzml_file}"]
    indexed_file = Dir["#{tmpdir}/*"][0]
    FileUtils.mv(indexed_file, mzml_file)
  end
end

.unindexed_mzml?(mzml_file) ⇒ Boolean

Returns:

  • (Boolean)

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# File 'lib/protk/convert_util.rb', line 21

def self.unindexed_mzml?(mzml_file)
  reader = LibXML::XML::Reader.file(mzml_file)
  reader.read
  reader.name == "mzML"
end