Class: MS::Troll

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/sim_trollop.rb

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Troll

Returns a new instance of Troll.



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# File 'lib/ms/sim_trollop.rb', line 5

def initialize
  @opts = Trollop::options do
    version "mspire-simulator 0.0.1a (c) 2012 Brigham Young University"
    banner <<-EOS

    *********************************************************************
     Description: Simulates ms runs given protein fasta files. Outputs
     a mzML file.


    Usage:
         mspire-simulator [options] <filenames>+

    where [options] are:
    EOS
    opt :digestor, "Digestion Enzyme; one of: \n\t\targ_c,\n \t\tasp_n,
asp_n_ambic,
            chymotrypsin,\n \t\tcnbr,
            lys_c,\n \t\tlys_c_p,
            pepsin_a,\n\t\ttryp_cnbr,
            tryp_chymo,\n \t\ttrypsin_p,
            v8_de,\n \t\tv8_e,
            trypsin,\n \t\tv8_e_trypsin,
            v8_de_trypsin",
            :default => "trypsin" 
            opt :missed_cleavages, "Number of missed cleavages during digestion", :default => 2
            opt :sampling_rate, "How many scans per second", :default => 0.5 
            opt :run_time, "Run time in seconds", :default => 1000.0 
            opt :noise, "Noise on or off", :default => "true"
            opt :noise_density, "Determines the density of white noise", :default => 10
            opt :noiseMaxInt, "The max noise intensity level", :default => 1000
            opt :noiseMinInt, "The minimum noise intensity level", :default => 50
            opt :pH, "The pH that the sample is in - for determining charge", :default => 2.6
            opt :out_file, "Name of the output file", :default => "test.mzml"
            opt :contaminants, "Fasta file containing contaminant sequences", :default => "testFiles/contam/hum_keratin.fasta"
            opt :dropout_percentage, "Defines the percentage of random dropouts in the run. 0.0 <= percentage < 1.0", :default => 0.01
            opt :shuffle, "Option shuffles the scans to simulate 1d data", :default => "false"
            opt :one_d, "Turns on one dimension simulation; run_time is automatically set to 300.0", :default => "false"
            opt :truth, "Determines truth file type; false gives no truth file; one of: 'xml' or 'csv' or 'xml_csv' (for both)", :default => "csv"
            opt :front, "Fronting chromatography parameter", :default => 6.65
            opt :tail, "Tailing chromatography parameter", :default => 0.30
            opt :mu, "Expected value of the chromatography curve", :default => 25.0
            opt :wobA, "m/z wobble parameter", :default => 0.001071
            opt :wobB, "m/z wobble parameter", :default => -0.5430
            opt :jagA, "intensity variance parameter", :default => 10.34
            opt :jagC, "intensity variance parameter", :default => 0.00712
            opt :jagB, "intensity variance parameter", :default => 0.12
            opt :overlapRange, "range in which to determine overlapping peaks", :default => 1.0724699230489427
            opt :email, "Email address to send completion messages to", :default => "nil"
            opt :mzml, "Mzml file to extract simulation parameters from", :default => "nil"
            opt :generations, "If an mzml file is provided this specifies the number of generations for the curve fitting algorithm", :default => 30000
            opt :mass_label, "Specify a mass tag pattern", :default => 0
            opt :ms2s, "Number of peptide ms2s to perform on each scan", :default => 1
            opt :ms2, "Turn on/off ms2 (true == on)", :default => "true"
            opt :databaseName, "Name of database file", :default => "peptides_[Time.now.sec]"
            opt :memory, "Determines whether to store the database in memory or write to file (false == write to file) Note: if true no database file will be accessible after simulation", :default => "false"
            opt :modifications, "To define residue or termini modifications. Enter a string Id1R1_Id2R2_ ... where Idi is a modification Id from http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo and Ri is the residue/terminus to apply it to (c-term = CT, n-term = NT)", :default => "false"

  end

  if @opts[:mzml] != "nil"
    @opts = CurveFit.get_parameters(@opts)
  end
  Trollop::die :sampling_rate, "must be greater than 0" if @opts[:sampling_rate] <= 0
  Trollop::die :run_time, "must be non-negative" if @opts[:run_time] < 0
  Trollop::die "must supply a .fasta protein sequence file" if ARGV.empty?
  Trollop::die :dropout_percentage, "must be between greater than or equal to 0.0 or less than 1.0" if @opts[:dropout_percentage] < 0.0 or @opts[:dropout_percentage] >= 1.0
  @opts[:overlapRange] = (@opts[:overlapRange]*10.0**-6)/2.0
end

Instance Method Details

#get ⇒ Object 



75
 
# File 'lib/ms/sim_trollop.rb', line 75

def get; @opts; end