MSAbundanceSim 0.2.0

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data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in MSAbundanceSim.gemspec
+gemspec

data/LICENSE

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+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    {one line to give the program's name and a brief idea of what it does.}
+    Copyright (C) {year}  {name of author}
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    {project}  Copyright (C) {year}  {fullname}
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

data/MSAbundanceSim.gemspec

@@ -0,0 +1,27 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ms_abundance_sim'
+
+Gem::Specification.new do |spec|
+  spec.name          = "MSAbundanceSim"
+  spec.version       = MSAbundanceSim::VERSION
+  spec.authors       = ["Rob Smith, John T. Prince"]
+  spec.email         = ["2robsmith@gmail.com", "jtprince@gmail.com"]
+
+  spec.summary       = %q{Simulate protein abundances.}
+  spec.description   = %q{Simulate protein abundances given FASTA files.}
+  spec.homepage      = "https://github.com/optimusmoose/MSAbundanceSim"
+  spec.licenses      = ['GPL-3.0']
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.13"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "minitest", "~> 5.0"
+end

data/README.md

@@ -0,0 +1,23 @@
+# MSAbundanceSim
+
+A simulator for creating case and control "samples" (molecule and abundance
+lists) in simple or .fasta format with reasonable variance from one or more
+real world examples.
+
+# Install
+
+    gem install MSAbundanceSim
+
+# Usage
+
+For help using the executable, type:
+
+    msabundancesim
+
+# Standalone usage:
+
+In cases where gems are not convenient, the file `lib/ms_abundance_sim.rb` may
+be used as its own standalone executable with no additional dependencies:
+
+    chmod +x lib/ms_abundance_sim.rb
+    ./lib/ms_abundance_sim.rb

data/Rakefile

@@ -0,0 +1,11 @@
+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList['test/**/*_test.rb']
+  t.warning = false
+end
+
+task :default => :test

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "ms_abundance_sim"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/exe/msabundancesim

@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+
+require "ms_abundance_sim"
+
+MSAbundanceSim::Commandline.run(ARGV)

data/lib/ms_abundance_sim.rb

@@ -0,0 +1,302 @@
+#!/usr/bin/env ruby
+#
+# Authors: (primary) Rob Smith and (secondary) John T. Prince
+# Released under GNU GPLv3
+# Contact Rob Smith at robert.smith@mso.umt.edu for other licensing options.
+
+require 'optparse'
+require 'set'
+require 'yaml'
+
+class MSAbundanceSim
+  VERSION = "0.2.0"
+end
+
+ProteinEntry = Struct.new(:entry_line_wo_abundance, :abundances, :additional_lines) do
+  def initialize(*args)
+    super(*args)
+    self.additional_lines ||= []
+  end
+end
+
+class Integer
+  def factorial
+    # https://www.rosettacode.org/wiki/Factorial#Ruby (fastest and most concise)
+    (2..self).reduce(1, :*)
+  end
+end
+
+class MSAbundanceSim
+  DEFAULTS = {
+    num_control: 5,
+    num_case: 5,
+    pct_diff_express: 3.0,
+    control_variance: 1,
+    case_variance: 2,
+    output_abundance_separator: " #",
+    downshift_min_threshold: 0,
+    downshift_probability_threshold: 0.75,
+    downshift_amount: 1,
+  }
+
+  class << self
+    # returns a Hash keyed by filenames and pointing to the output of
+    # process_file (a list of case and control filenames, keyed by 'case' and
+    # 'control')
+    def process_files(filenames, opts)
+      outputs = filenames.map do |filename|
+        MSAbundanceSim.new.process_file(filename, opts)
+      end
+      filenames.zip(outputs).to_h
+    end
+
+    # event_rate (lambda)
+    # num_occurences (k)
+    def poisson(event_rate, num_occurences)
+      return event_rate**num_occurences * Math.exp(-event_rate) / num_occurences.factorial.to_f
+    end
+
+    # probability (y)
+    def inverse_transform_sample(event_rate)
+      max = poisson(event_rate, event_rate)
+      probability = rand * (max)
+      list_of_num_occurrences = (0..event_rate*4).to_a.shuffle # attempt to capture the entire distribution without wasting tests
+      list_of_num_occurrences.each do |num_occurences|
+        p_num_occurences = poisson(event_rate, num_occurences)
+        return num_occurences if probability < p_num_occurences
+      end
+      puts "Problem: Should have found a num_occurences in inverse_transform_sample"
+    end
+
+    def get_fold_change(a_i, event_rate, max_abundance)
+      # max fold change at lowest abundance
+      raw_fc = inverse_transform_sample(event_rate)
+      norm_fc = raw_fc * (1.0-(a_i[0].to_f / max_abundance))
+      pert_fc = norm_fc * rand
+      sign = [1,-1].sample
+      return pert_fc * sign
+    end
+
+    # takes 'value' and subtracts 'amount' from it if 'value' is greater than
+    # min_threshold AND a random number is less than the probability_threshold
+    # (i.e., a probability of 1 means downshifting will happen to all values).
+    def downshift(value, min_threshold, probability_threshold, amount, random=rand())
+      if (value > min_threshold) && (random < probability_threshold)
+        value - amount
+      else
+        value
+      end
+    end
+
+    def sample_abundance(abundances, fold_change)
+      abundance = 0.0
+      if abundances.size > 1 # linear interpolation
+        idx = [1..abundances.size-1].sample(1)
+        next_idx = idx+1 < abundances.size ? idx+1 : abundances[0] # edge case: 2 abundances
+        abundance = abundances[idx] + rand * (abundances[next_idx] - abundances[idx])
+      else # sample w/variance
+        if fold_change >= 0 # positive fold change
+          abundance = abundances[0].to_f * fold_change + abundances[0]
+        else # negative fold change
+          fold_change *= -1
+          abundance = abundances[0] / (2.0**fold_change)
+        end
+      end
+      return abundance + [1,-1].sample * rand * 0.1 * abundance
+    end
+  end
+
+  def process_file(filename, opts)
+    opts = DEFAULTS.merge(opts)
+
+    basename = filename.chomp(File.extname(filename))
+
+    protein_entries = get_protein_entries(filename)
+    max_abundance = protein_entries.max_by {|entry| entry.abundances.last }.abundances.last
+
+    # generate which proteins will be differentially expressed
+    num_proteins_to_diff_express = (protein_entries.size * opts[:pct_diff_express]/100.0).to_i
+    diff_expressed_ids = (0...protein_entries.size).to_a.sample(num_proteins_to_diff_express).to_set
+
+    output = Hash.new {|hash, key| hash[key] = [] }
+    case_and_controls_needed = ([:case] * opts[:num_case]) + ([:control] * opts[:num_control])
+    case_and_controls_needed.each_with_index do |sample_type, sample_number| # for each sample
+      outfilename = "#{basename}_#{sample_number}_#{sample_type}"
+      output[sample_type] << outfilename
+      File.open(outfilename, 'w') do |outfile|
+        protein_entries.each_with_index do |protein_entry, idx|
+          # put first line of fasta with simulated abundance
+          variance = opts[
+            if sample_type == :case && diff_expressed_ids.include?(idx)
+              :case_variance
+            else
+              :control_variance
+            end
+          ]
+
+          fold_change = MSAbundanceSim.get_fold_change(protein_entry.abundances, variance, max_abundance)
+
+          downshift_params = %w(min_threshold probability_threshold amount)
+            .map {|key| 'downshift_' + key }
+            .map(&:to_sym)
+            .map {|key| opts[key] }
+
+          downshifted_fold_change = MSAbundanceSim.downshift(fold_change, *downshift_params)
+
+          sample_abundance = MSAbundanceSim.sample_abundance(protein_entry.abundances, downshifted_fold_change)
+          outfile.puts [protein_entry.entry_line_wo_abundance, sample_abundance].join(opts[:output_abundance_separator])
+          outfile.puts protein_entry.additional_lines.join("\n")
+        end
+      end
+    end
+    output
+  end
+
+  # returns an array with the beginning part of the entry line (without the
+  # abundance (which begins with a '#') and an array of abundances (all the
+  # numbers, returned as Floats, after the final '#')
+  def parse_entry_line(line)
+    octothorpe_index = line.rindex("#")
+    entry_line_wo_abundance = line[0...octothorpe_index]
+    abundance_str = line[(octothorpe_index+1)..-1]
+    abundances = abundance_str.split(",").map(&:to_f).sort
+    [entry_line_wo_abundance, abundances]
+  end
+
+  def get_protein_entries(filename)
+    protein_entries = []
+    IO.foreach(filename) do |line|
+      line.chomp!
+      if line[0] == ">"
+        protein_entries << ProteinEntry.new(*parse_entry_line(line))
+      else
+        protein_entries.last.additional_lines << line
+      end
+    end
+    protein_entries
+  end
+
+  class Commandline
+    class << self
+      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
+
+      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
+
+      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(
+            "--downshift-amount<#{defaults[:downshift_amount]}>",
+            Float,
+            "Amount the fold change will be altered",
+            "if meeting the threshold and probability-",
+            "threshold."
+          ) {|v| opts[:downshift_amount] = v }
+
+          op.on("--verbose", "talk about it") {|v| $VERBOSE = 3 }
+        end
+        [parser, opts]
+      end
+    end
+  end
+end
+
+if __FILE__ == $0
+  MSAbundanceSim::Commandline.run(ARGV)
+end
+
+

data/scripts/crawler.rb

@@ -0,0 +1,54 @@
+require 'rubygems'
+require 'nokogiri'
+require 'open-uri'
+
+DATA_DIR = "fastas"
+Dir.mkdir(DATA_DIR) unless File.exists?(DATA_DIR)
+
+base_url = "http://pax-db.org/protein/"
+
+# load ids and abundances
+molecules = []
+infile = File.open("9606-PA_plasma.txt","r")
+while line = infile.gets
+	unless line[0] == '#' # header
+		parts = line.chop.split(" ")
+		molecules << [parts[0],parts[2]]
+	end
+end
+infile.close
+
+outfile = File.open("9606-PA_plasma.fasta","w")
+log = File.open("9606-PA_plasma.log","w")
+
+molecules.each_w_index do |molecule, m_idx|
+	puts "Building #{m_idx} of #{molecules.size}"
+
+	#go to pax-db page for this molecule
+	page = Nokogiri::HTML(open("#{base_url}#{molecule[0]}"))
+
+	#get uniprot page link
+	link = page.xpath("/html/body/div[2]/p/a")[0].attributes["href"].value
+
+	#pull fasta entry from uniprot
+	uniprot_molecule_page = ""
+	begin
+	uniprot_molecule_page = Nokogiri::HTML(open(link))
+
+	fasta_link = uniprot_molecule_page.css("//div#sequences.section div#sequences-section div.sequence-isoform div.sequence-isoform-leftcol a.tooltipped.icon.icon-functional.button.displayThis")[0].attributes["href"]
+
+	fasta = Nokogiri::HTML(open("http://uniprot.org#{fasta_link}")).elements[0].child.child.child.text
+
+	#write out fasta file, inserting standard abundance
+	fasta_lines = fasta.split("\n")
+	outfile.puts "#{fasta_lines[0]} ##{molecule[1]}" 
+	fasta_lines[1..-1].each do |fasta_line|
+		outfile.puts fasta_line
+	end
+	rescue
+		log.puts "Failed to open #{link}"
+	end
+end
+
+outfile.close
+log.close

metadata

@@ -0,0 +1,98 @@
+--- !ruby/object:Gem::Specification
+name: MSAbundanceSim
+version: !ruby/object:Gem::Version
+  version: 0.2.0
+platform: ruby
+authors:
+- Rob Smith, John T. Prince
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-05-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.13'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.13'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+description: Simulate protein abundances given FASTA files.
+email:
+- 2robsmith@gmail.com
+- jtprince@gmail.com
+executables:
+- msabundancesim
+extensions: []
+extra_rdoc_files: []
+files:
+- Gemfile
+- LICENSE
+- MSAbundanceSim.gemspec
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- exe/msabundancesim
+- lib/ms_abundance_sim.rb
+- scripts/crawler.rb
+homepage: https://github.com/optimusmoose/MSAbundanceSim
+licenses:
+- GPL-3.0
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.11
+signing_key: 
+specification_version: 4
+summary: Simulate protein abundances.
+test_files: []