Class: MSAbundanceSim::Commandline

Inherits:

Object

• Object
• MSAbundanceSim::Commandline

Defined in:

lib/ms_abundance_sim.rb

Class Method Summary

• .create_parser ⇒ Object
• .format_and_emit_output(output) ⇒ Object
• .run(argv) ⇒ Object

Class Method Details

.create_parser ⇒ Object

# File 'lib/ms_abundance_sim.rb', line 202

def create_parser
  defaults = MSAbundanceSim::DEFAULTS
  opts = MSAbundanceSim::DEFAULTS
  parser = OptionParser.new do |op|
    op.banner = "usage: #{File.basename(__FILE__)} [options] <file>.fasta ..."
    op.separator "generates files, each of this form: <file>_<n>_<case|control>"
    op.separator "  where the specified percentage of proteins have altered abundance (for cases)."
    op.separator ""
    op.separator "output: (yaml indicating all the related derivative files)"
    op.separator "  for 2 cases and 1 control the output for file.fasta would be: "
    op.separator "    file.fasta:"
    op.separator "      case:"
    op.separator "      - file_0_case"
    op.separator "      - file_1_case"
    op.separator "      control:"
    op.separator "      - file_2_control"
    op.separator ""
    op.separator "The file must have one or more abundances per protein entry (the protein"
    op.separator "sequence following the header line is optional)."
    op.separator "The abundance is placed at the end of the line following a ' #',"
    op.separator "with multiple abundances separated with a ','.  Here are two examples:"
    op.separator ""
    op.separator "> SWISSAB|23B The anchor protein #23.2"
    op.separator "> SWISSSPECIAL|24B A green protein #23.2,29.4"
    op.separator ""
    op.separator "notes: Protein sequences are optional and files need not end in '.fasta'"
    op.separator ""
    op.separator "options (<default>):"

    op.on(
      "--num-control <#{defaults[:num_control]}>",
      Integer,
      "Number of *control* samples to generate."
    ) {|v| opts[:num_control] = v }

    op.on(
      "--num-case <#{defaults[:num_case]}>",
      Integer,
      "Number of *case* samples to generate."
    ) {|v| opts[:num_case] = v }

    op.on(
      "--pct-diff-express <#{defaults[:pct_diff_express]}>",
      Float,
      "Percentage of proteins to differentially ",
      "  express between case and control."
    ) {|v| opts[:pct_diff_express] = v }

    op.on(
      "--control-variance <#{defaults[:control_variance]}>",
      Integer,
      "Variance for control samples (max lambda for",
      "  Poisson distribution). The higher the value, ",
      "  the more fold change will occur among healthy ",
      "  populations. Used only when multiple ",
      "  abundances are not provided in master fasta. ",
      "  Not recommended to modify this parameter."
    ) {|v| opts[:control_variance] = v }

    op.on(
      "--case-variance <#{defaults[:case_variance]}>",
      Integer,
      "Variance increase for case samples (max lambda ",
      "  for Poisson distribution). The higher the ",
      "  value the more fold change will occur."
    ) {|v| opts[:case_variance] = v }

    op.on(
      "--downshift-min-threshold<#{defaults[:downshift_min_threshold]}>",
      Float,
      "Min threshold for downshifting some fold changes."
    ) {|v| opts[:downshift_min_threshold] = v }

    op.on(
      "--downshift-probability-threshold<#{defaults[:downshift_probability_threshold]}>",
      Float,
      "Min probability threshold for downshifting",
      "some fold changes."
    ) {|v| opts[:downshift_probability_threshold] = v }

    op.on("--verbose", "talk about it") {|v| $VERBOSE = 3 }
  end
  [parser, opts]
end

.format_and_emit_output(output) ⇒ Object

# File 'lib/ms_abundance_sim.rb', line 195

def format_and_emit_output(output)
  # the type keys are symbols--make them strings
  output_string_types = output.map {|key, value| [key, value.map {|k, v| [k.to_s, v] }.to_h] }.to_h
  # emit yaml without leading "---"
  puts output_string_types.to_yaml.gsub(/\A---\n/, '')
end

.run(argv) ⇒ Object

# File 'lib/ms_abundance_sim.rb', line 181

def run(argv)
  parser, opts = create_parser
  parser.parse!(argv)

  filenames = argv.to_a

  if filenames.size == 0
    puts parser
  else
    output = MSAbundanceSim.process_files(filenames, opts)
    format_and_emit_output(output)
  end
end