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 "\n    *********************************************************************\n     Description: Simulates ms runs given protein fasta files. Outputs\n     a mzML file.\n\n\n    Usage:\n         mspire-simulator [options] <filenames>+\n\n    where [options] are:\n    EOS\n    opt :digestor, \"Digestion Enzyme; one of: \\n\\t\\targ_c,\\n \\t\\tasp_n,\nasp_n_ambic,\n            chymotrypsin,\\n \\t\\tcnbr,\n            lys_c,\\n \\t\\tlys_c_p,\n            pepsin_a,\\n\\t\\ttryp_cnbr,\n            tryp_chymo,\\n \\t\\ttrypsin_p,\n            v8_de,\\n \\t\\tv8_e,\n            trypsin,\\n \\t\\tv8_e_trypsin,\n            v8_de_trypsin\",\n            :default => \"trypsin\" \n            opt :missed_cleavages, \"Number of missed cleavages during digestion\", :default => 2\n            opt :sampling_rate, \"How many scans per second\", :default => 0.5 \n            opt :run_time, \"Run time in seconds\", :default => 1000.0 \n            opt :noise, \"Noise on or off\", :default => \"true\"\n            opt :noise_density, \"Determines the density of white noise\", :default => 10\n            opt :noiseMaxInt, \"The max noise intensity level\", :default => 1000\n            opt :noiseMinInt, \"The minimum noise intensity level\", :default => 50\n            opt :pH, \"The pH that the sample is in - for determining charge\", :default => 2.6\n            opt :out_file, \"Name of the output file\", :default => \"test.mzml\"\n            opt :contaminants, \"Fasta file containing contaminant sequences\", :default => \"testFiles/contam/hum_keratin.fasta\"\n            opt :dropout_percentage, \"Defines the percentage of random dropouts in the run. 0.0 <= percentage < 1.0\", :default => 0.01\n            opt :shuffle, \"Option shuffles the scans to simulate 1d data\", :default => \"false\"\n            opt :one_d, \"Turns on one dimension simulation; run_time is automatically set to 300.0\", :default => \"false\"\n            opt :truth, \"Determines truth file type; false gives no truth file; one of: 'xml' or 'csv' or 'xml_csv' (for both)\", :default => \"csv\"\n            opt :front, \"Fronting chromatography parameter\", :default => 6.65\n            opt :tail, \"Tailing chromatography parameter\", :default => 0.30\n            opt :mu, \"Expected value of the chromatography curve\", :default => 25.0\n            opt :wobA, \"m/z wobble parameter\", :default => 0.001071\n            opt :wobB, \"m/z wobble parameter\", :default => -0.5430\n            opt :jagA, \"intensity variance parameter\", :default => 10.34\n            opt :jagC, \"intensity variance parameter\", :default => 0.00712\n            opt :jagB, \"intensity variance parameter\", :default => 0.12\n            opt :overlapRange, \"range in which to determine overlapping peaks\", :default => 1.0724699230489427\n            opt :email, \"Email address to send completion messages to\", :default => \"nil\"\n            opt :mzml, \"Mzml file to extract simulation parameters from\", :default => \"nil\"\n            opt :generations, \"If an mzml file is provided this specifies the number of generations for the curve fitting algorithm\", :default => 30000\n            opt :mass_label, \"Specify a mass tag pattern\", :default => 0\n            opt :ms2s, \"Number of peptide ms2s to perform on each scan\", :default => 1\n            opt :ms2, \"Turn on/off ms2 (true == on)\", :default => \"true\"\n            opt :databaseName, \"Name of database file\", :default => \"peptides_[Time.now.sec]\"\n            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\"\n            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\"\n\n  end\n\n  if @opts[:mzml] != \"nil\"\n    @opts = CurveFit.get_parameters(@opts)\n  end\n  Trollop::die :sampling_rate, \"must be greater than 0\" if @opts[:sampling_rate] <= 0\n  Trollop::die :run_time, \"must be non-negative\" if @opts[:run_time] < 0\n  Trollop::die \"must supply a .fasta protein sequence file\" if ARGV.empty?\n  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\n  @opts[:overlapRange] = (@opts[:overlapRange]*10.0**-6)/2.0\nend\n"

Instance Method Details

#get ⇒ Object 



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

def get; @opts; end