Class: MzMLParser

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

Instance Method Summary collapse

Constructor Details

#initialize(path) ⇒ MzMLParser

Returns a new instance of MzMLParser.



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# File 'lib/protk/mzml_parser.rb', line 8

def initialize(path)
  @namespace=
  @mzml_ns_prefix="xmlns:"
  @mzml_ns="xmlns:http://psi.hupo.org/ms/mzml"

  doc=XML::Document.file(path)
  @file_reader=XML::Reader.document(doc)
end

Instance Method Details

#next_runid ⇒ Object 



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# File 'lib/protk/mzml_parser.rb', line 17

def next_runid()
  until @file_reader.name=="run" 
    if !@file_reader.read()
      return nil
    end
  end
  return @file_reader.get_attribute('id')
end

#next_spectrum ⇒ Object 



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# File 'lib/protk/mzml_parser.rb', line 26

def next_spectrum()

  until @file_reader.name=="spectrum" 
    if !@file_reader.read()
      return nil
    end
  end

  this_spect=spectrum_as_hash(@file_reader.expand)

  @file_reader.next_sibling

  return this_spect
end

#spectrum_as_hash(spectrum) ⇒ Object 



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# File 'lib/protk/mzml_parser.rb', line 41

def spectrum_as_hash(spectrum)
  index=spectrum.attributes['index']
  sid = spectrum.attributes['id']
  precursor_mz_param = spectrum.find(".//#{@mzml_ns_prefix}cvParam[@accession=\"MS:1000744\"]",@mzml_ns)[0]
  mslevel_param = spectrum.find("./#{@mzml_ns_prefix}cvParam[@accession=\"MS:1000511\"]",@mzml_ns)[0]

  title_param = spectrum.find("./#{@mzml_ns_prefix}cvParam[@accession=\"MS:1000796\"]",@mzml_ns)[0]

  # prec_mz = spectrum.find(".//#{@mz}")

  precursor_mz_mz = precursor_mz_param.attributes['value'] if precursor_mz_param
  mslevel = mslevel_param.attributes['value'] if mslevel_param
  spectrum_title = title_param['value'] if title_param

  data_arrays = spectrum.find("./#{@mzml_ns_prefix}binaryDataArrayList/#{@mzml_ns_prefix}binaryDataArray",@mzml_ns)

  data={}
  data_arrays.each do |arr|
    the_data = arr.find("./#{@mzml_ns_prefix}binary",@mzml_ns)[0].content
    mzaccession = arr.find("./#{@mzml_ns_prefix}cvParam[@accession=\"MS:1000514\"]",@mzml_ns)
    if ( mzaccession.length==1 )
      data[:mz] = the_data
    else 
      data[:intensity] = the_data
    end
  end
  data[:title]=spectrum_title
  data[:mzlevel]=mslevel
  data[:index]=index
  data[:precursormz]=precursor_mz_mz
  data[:id]=sid

  data
end