Class: Ms::Xcalibur::Peakify

Inherits:
Tap::Tasks::FileTask
  • Object
show all
Defined in:
lib/ms/xcalibur/peakify.rb

Overview

:startdoc::task adds graph data to an exported peak file

Peakify adds points to signify the relative intensity (ie the rounded intensity/max_intensity) of peaks to a peak list extracted from Xcalibur Qual Browser (v 2.0).. This can be useful as a visual aid. 

[peakfile.txt]
SPECTRUM - MS
GSE_T29K_080703143635.raw
ITMS + c ESI Full ms [300.00-2000.00]
Scan #: 11
RT: 0.07
Data points: 1490
Mass	Intensity
300.516479	2000.0	.................................
301.392487	1000.0	.................
302.465759	3000.0	..................................................
...

Options can be specified to filter out points within a range of relative intensities.

Instance Method Summary collapse

Instance Method Details

#process(source) ⇒ Object 



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# File 'lib/ms/xcalibur/peakify.rb', line 36

def process(source)
  prepare(output) if output.kind_of?(String)
  open_io(output, 'w') do |target|
    target.binmode
    
    # now perform the task...
    peak_file = PeakFile.parse File.read(source)
    max_intensity = peak_file.data.inject(0) do |max, (mz, intensity)|
      intensity > max ? intensity : max
    end

    range = min..max
    peak_file.data = peak_file.data.collect do |(mz, intensity)|
      percent = (intensity / max_intensity * 100)
      next unless range.include?(percent)

      [mz, intensity, point_char * percent.round]
    end.compact

    if sort
      peak_file.data = peak_file.data.sort_by do |(mz, intensity)|
        intensity
      end.reverse
    end

    target << peak_file.to_s
  end
  output
end