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Contents
require 'spec_helper'
require 'ms/mzml'
require 'ms/mzml/plms1'
describe 'converting mzml to plms1' do
describe 'converting no spectra mzml' do
before do
@mzml_file = File.open( TESTFILES + "/ms/mzml/openms.noidx_nocomp.12.mzML" )
@mzml = MS::Mzml.new(@mzml_file)
end
after do
@mzml_file.close
end
it 'can be converted into a plms1 object' do
scan_nums = (10929..10940).to_a
times =[6604.58, 6605.5, 6605.91, 6606.48, 6606.98, 6607.53, 6607.93, 6608.49, 6608.92, 6609.49, 6609.94, 6610.53]
plms1 = @mzml.to_plms1
plms1.spectra.respond_to?(:each).should be_true
plms1.times.should == times
plms1.scan_numbers.should == scan_nums
plms1.spectra.each do |spec|
spec.size.should == 2
spec.class.should == MS::Spectrum
spec.mzs.should == []
spec.intensities.should == []
end
#plms1.write("tmp.tmp.bin")
end
end
describe 'converting normal mzml' do
before do
@mzml_file = File.open( TESTFILES + "/ms/mzml/j24z.idx_comp.3.mzML" )
@mzml = MS::Mzml.new(@mzml_file)
end
after do
@mzml_file.close
end
it 'can be converted into a plms1 object' do
#scan_nums = ###
#times =[6604.58, 6605.5, 6605.91, 6606.48, 6606.98, 6607.53, 6607.93, 6608.49, 6608.92, 6609.49, 6609.94, 6610.53]
plms1 = @mzml.to_plms1
plms1.spectra.respond_to?(:each).should be_true
plms1.times.should == [1981.5726, 1982.1077, 1982.4020999999998]
plms1.scan_numbers.should == [1, 2, 3]
sizes = [20168, 315, 634]
plms1.spectra.zip(sizes).each do |spec,exp_size|
spec.class.should == MS::Spectrum
spec.size.should == 2
spec.mzs.size.should == exp_size
spec.intensities.size.should == exp_size
end
#plms1.write("tmp.tmp.bin")
end
end
end
Version data entries
7 entries across 7 versions & 1 rubygems