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_spectrum ⇒ Object 



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

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 32

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