Class: Xcalibur::Peakify

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

Overview

:startdoc::manifest adds graph data to an exported peak file Peakify adds points to signify the relative intensity (ie the rounded intensity/max_intensity) of peaks in an exported peak list. This can be useful as a visual aid. 

[a_sample_result.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. Peakify can handle exported peak lists from Xcalibur Qual Browser (v 2.0).

Instance Method Summary collapse

Instance Method Details

#process(filepath) ⇒ Object 



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# File 'lib/xcalibur/peakify.rb', line 33

def process(filepath)
  target = app.filepath(:data, "peak_#{File.basename(filepath)}" )
  prepare(target) 
  
  # now perform the task...
  peak_file = PeakFile.parse File.read(filepath)
  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
  
  File.open(target, "wb") do |file|
    file << peak_file.to_s
  end
  
  target
end