aai 0.1.0

checksums.yaml

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+SHA1:
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+  data.tar.gz: 3cfbfb4aa4a9371f470cd129dc32ab9dcffd1838
+SHA512:
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data/.coveralls.yml

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+service_name: travis-ci

data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status

data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.0
+  - 2.1
+  - 2.2
+  - 2.3
+  - 2.4
+before_install: gem install bundler -v 1.14.6

data/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at moorer@udel.edu. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

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

data/LICENSE

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+MIT License
+
+Copyright (c) 2017 Ryan Moore
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# AAI
+
+[![Build Status](https://travis-ci.org/mooreryan/aai.svg?branch=master)](https://travis-ci.org/mooreryan/aai)
+[![Coverage Status](https://coveralls.io/repos/github/mooreryan/aai/badge.svg?branch=master)](https://coveralls.io/github/mooreryan/aai?branch=master)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Calculate Seanie's multi-genome (or genome bin) amino acid similarity.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'aai'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install aai
+
+## Requirements
+
+- GNU Parallel
+- NCBI Blast suite
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/aai. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/aai.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'aai/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "aai"
+  spec.version       = Aai::VERSION
+  spec.authors       = ["Ryan Moore"]
+  spec.email         = ["moorer@udel.edu"]
+
+  spec.summary       = %q{Seanie's amino acid similarity.}
+  spec.description   = %q{Calculate Seanie's amino acid similarity score between multiple genomes/bins.}
+  spec.homepage      = "https://github.com/mooreryan/aai.git"
+  spec.license       = "MIT"
+
+  # Prevent pushing this gem to RubyGems.org. To allow pushes either set the 'allowed_push_host'
+  # to allow pushing to a single host or delete this section to allow pushing to any host.
+  # if spec.respond_to?(:metadata)
+  #   spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com'"
+  # else
+  #   raise "RubyGems 2.0 or newer is required to protect against " \
+  #     "public gem pushes."
+  # end
+
+  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", "~> 1.14"
+  spec.add_development_dependency "coveralls", "~> 0.8.21"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "yard", "~> 0.9.9"
+
+  spec.add_runtime_dependency "abort_if", "~> 0.2.0"
+  spec.add_runtime_dependency "parse_fasta", "~> 2.2"
+  spec.add_runtime_dependency "systemu", "~> 2.6", ">= 2.6.5"
+  spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.2"
+end

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "aai"
+
+# 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(__FILE__)

data/bin/setup

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+#!/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/aai.rb

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+#!/usr/bin/env ruby
+
+Signal.trap("PIPE", "EXIT")
+
+require "aai"
+require "abort_if"
+require "fileutils"
+require "trollop"
+
+include AbortIf
+include AbortIf::Assert
+
+Aai.extend Aai
+Aai.extend Aai::Utils
+
+version_banner =
+
+opts = Trollop.options do
+  version Aai::VERSION_BANNER
+
+  banner <<-EOS
+
+#{Aai::VERSION_BANNER}
+
+  Seanie's AAI calculator.
+
+  Each input file is treated as a file of ORFs for a single genome.
+
+  Options:
+  EOS
+
+  opt(:infiles, "Input files", type: :strings)
+  opt(:outdir, "Output directory", type: :string, default: ".")
+  opt(:basename, "Base name for output file", type: :string,
+      default: "aai_scores")
+end
+
+abort_if opts[:infiles].nil? || opts[:infiles].empty?,
+         "No infiles given"
+
+Aai.check_files opts[:infiles]
+
+FileUtils.mkdir_p opts[:outdir]
+
+seq_lengths, clean_fnames = Aai.process_input_seqs! opts[:infiles]
+
+blast_db_basenames = Aai.make_blastdbs! clean_fnames
+
+btabs = Aai.blast_permutations! clean_fnames, blast_db_basenames
+
+best_hits = Aai.get_best_hits btabs, seq_lengths
+
+one_way = Aai.one_way_aai best_hits
+
+two_way = Aai.two_way_aai best_hits
+
+aai_strings = Aai.aai_strings one_way, two_way
+
+outf = File.join opts[:outdir], "#{opts[:basename]}.aai.txt"
+File.open(outf, "w") do |f|
+  Aai.aai_strings(one_way, two_way).each do |str|
+    f.puts str
+  end
+end

data/lib/aai.rb

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+require "abort_if"
+require "systemu"
+require "parse_fasta"
+
+require "aai/core_extensions"
+require "aai/utils"
+require "aai/version"
+
+AbortIf.extend AbortIf
+Process.extend Aai::CoreExtensions::Process
+
+module Aai
+  include Utils
+
+  BLAST_DB_SEPARATOR = "...."
+  BLAST_DB_SUFFIX    = "#{BLAST_DB_SEPARATOR}aai"
+
+  PIDENT_CUTOFF = 30
+  EVALUE_CUTOFF = 1e-3
+  LENGTH_CUTOFF = 70 # actually is 70 percent
+
+  def blast_permutations! fastas, blast_dbs
+    file_permutations = one_way_combinations fastas, blast_dbs, true
+    file_permutations = file_permutations.select do |f1, f2|
+      genome_from_fname(f1) != genome_from_fname(f2)
+    end
+
+    first_files = file_permutations.map(&:first)
+    second_files = file_permutations.map(&:last)
+
+    first_genomes = first_files.map do |fname|
+      ary = fname.split(".")
+      ary.take(ary.length - 1).join
+    end
+
+    second_genomes = second_files.map do |fname|
+      ary = fname.split(BLAST_DB_SEPARATOR).take(1)
+      AbortIf.abort_unless ary.length == 1,
+                   "Bad file name for #{fname}"
+
+      ary = ary.first.split(".")
+
+      File.basename ary.take(ary.length - 1).join
+    end
+
+    outf_names = first_genomes.zip(second_genomes).map do |f1, f2|
+      "#{f1}____#{f2}.aai_blastp"
+    end
+
+    title = "Running blast jobs"
+    cmd = "parallel --link blastp -outfmt 6 " +
+          "-query {1} -db {2} " +
+          "-out {3} -evalue 1e-3 " +
+          "::: #{first_files.join " "} ::: " +
+          "#{second_files.join " "} ::: " +
+          "#{outf_names.join " "}"
+
+    Process.run_and_time_it! title, cmd
+
+    outf_names
+  end
+
+  # Make blast dbs given an array of filenames.
+  #
+  # @param fnames [Array<String>] an array of filenames
+  #
+  # @return [Array<String>] blast db basenames
+  def make_blastdbs! fnames
+    suffix = BLAST_DB_SUFFIX
+    outfiles = fnames.map { |fname| fname + suffix }
+
+    title = "Making blast databases"
+    cmd = "parallel makeblastdb -in {} " +
+          "-out {}#{BLAST_DB_SUFFIX} -dbtype prot " +
+          "::: #{fnames.join " "}"
+
+    Process.run_and_time_it! title, cmd
+
+    outfiles
+  end
+
+  # Returns a hash table with sequence lengths and writes new fasta
+  # files with clean headers for blast.
+  #
+  # The sequences are annotated with the genome that they came from.
+  #
+  # @param fnames [Array<String>] an array of fasta file names
+  def process_input_seqs! fnames
+    seq_lengths = {}
+    clean_fnames = []
+
+    fnames.each do |fname|
+      clean_fname = fname + "_aai_clean"
+      clean_fnames << clean_fname
+      File.open(clean_fname, "w") do |f|
+        Object::ParseFasta::SeqFile.open(fname).each_record do |rec|
+          header =
+            annotate_header clean_header(rec.header),
+                            File.basename(fname)
+
+          seq_lengths[header] = rec.seq.length
+
+          f.puts ">#{header}\n#{rec.seq}"
+        end
+      end
+    end
+
+    [seq_lengths, clean_fnames]
+  end
+
+  def get_best_hits fnames, seq_lengths
+    best_hits = {}
+    fnames.each do |fname| # blast files
+      File.open(fname, "rt").each_line do |line|
+        ary = line.chomp.split "\t"
+
+        query  = ary[0]
+        target = ary[1]
+        pident = ary[2].to_f
+        length = ary[3].to_f
+        evalue = ary[10].to_f
+
+        query_genome = query.split("____").first
+        query_seq    = query.split("____").last
+
+        target_genome = target.split("____").first
+        target_seq    = target.split("____").last
+
+        seq_length_key = "#{query_genome}____#{query_seq}"
+
+        AbortIf.abort_unless seq_lengths.has_key?(seq_length_key),
+                             "#{seq_length_key} is missing from " +
+                             "seq_lengths"
+
+        query_length = seq_lengths[seq_length_key].to_f
+        length_percent = length / query_length * 100
+
+        hit_info = {
+          query_name: query_seq,
+          target_name: target_seq,
+          query_genome: query_genome,
+          target_genome: target_genome,
+          pident: pident,
+          length: length_percent,
+          evalue: evalue
+        }
+
+        # check if it is a best hit candidate
+        if pident >= PIDENT_CUTOFF &&
+           evalue <= EVALUE_CUTOFF &&
+           length_percent >= LENGTH_CUTOFF
+
+          if best_hits.has_key? query_genome
+            if best_hits[query_genome].has_key? query_seq
+              if best_hits[query_genome][query_seq].
+                  has_key?(target_genome)
+                # check if we should replace the best hit?
+                current_best_hit =
+                  best_hits[query_genome][query_seq][target_genome]
+
+                if pident >= current_best_hit[:pident]
+                  best_hits[query_genome][query_seq][target_genome] =
+                    hit_info
+                end
+              else
+                best_hits[query_genome][query_seq][target_genome] =
+                  hit_info
+              end
+            else
+              best_hits[query_genome][query_seq] = {
+                target_genome => hit_info
+              }
+            end
+          else
+            best_hits[query_genome] = {
+              query_seq => {
+                target_genome => hit_info
+              }
+            }
+          end
+        else
+          # pass
+        end
+      end
+    end
+
+    best_hits
+  end
+
+  def one_way_aai best_hits
+    one_way_best_hits(best_hits).map do |genome_pair, best_hits|
+      [genome_pair, best_hits.map { |hit| hit[:pident] }.reduce(:+) /
+                    best_hits.length.to_f]
+    end.to_h
+  end
+
+  def two_way_aai best_hits
+    # the pair key is the [g1, g2].sort
+
+    two_way_aai = {}
+
+    one_way_hits = one_way_best_hits best_hits
+    genome_pair_keys = one_way_hits.keys.map { |pair| pair.sort }.uniq
+
+    genome_pair_keys.each do |pair_key|
+      AbortIf.abort_unless one_way_hits.has_key?(pair_key) &&
+                           one_way_hits.has_key?(pair_key.reverse),
+                           "Missing keys for #{pair_key}"
+
+      forward_hits = one_way_hits[pair_key]
+      reverse_hits = one_way_hits[pair_key.reverse]
+
+      combinations = one_way_combinations forward_hits, reverse_hits
+
+      two_way_hits = combinations.select do |h1, h2|
+        two_way_hit? h1, h2
+      end
+
+      two_way_hit_info = two_way_hits.map do |h1, h2|
+        { genome_pair: [h1[:query_genome],
+                        h1[:target_genome]].sort,
+          pident: (h1[:pident] + h2[:pident]) / 2.0 }
+      end
+
+      two_way_hit_info.each do |hit|
+        if two_way_aai.has_key? hit[:genome_pair]
+          two_way_aai[hit[:genome_pair]] << hit[:pident]
+        else
+          two_way_aai[hit[:genome_pair]] = [hit[:pident]]
+        end
+      end
+    end
+
+    two_way_aai.map do |genome_pair, pidents|
+      [genome_pair, pidents.reduce(:+) / pidents.length.to_f]
+    end.to_h
+  end
+
+  # Returns an array (enumerable) of aai strings ready to print
+  def aai_strings one_way_aai, two_way_aai
+    aai_strings = {}
+    keys = (one_way_aai.keys + two_way_aai.keys).
+           map { |key| key.sort }.uniq
+
+    keys.each do |key|
+      a_to_b_aai = one_way_aai[key] || "NA"
+      b_to_a_aai = one_way_aai[key.reverse] || "NA"
+      two_way = two_way_aai[key] || "NA"
+
+      aai_strings[key] = [a_to_b_aai,
+                          b_to_a_aai,
+                          two_way]
+    end
+
+    aai_strings.map do |genome_pair, aais|
+      [genome_pair.join("----"),
+       aais.join("\t")].join "\t"
+    end
+  end
+
+  private
+
+  def two_way_hit? hit1, hit2
+    hit1[:query_name] == hit2[:target_name] &&
+      hit1[:query_genome] == hit2[:target_genome]
+  end
+
+  def one_way_best_hits best_hits
+    one_way = {}
+
+    best_hits.each do |query_genome, orfs|
+      orfs.each do |orf, target_genomes|
+        target_genomes.each do |target_genome, best_hit|
+          genome_pair = [query_genome, target_genome]
+          if one_way.has_key? genome_pair
+            one_way[genome_pair] << best_hit
+          else
+            one_way[genome_pair] = [best_hit]
+          end
+        end
+      end
+    end
+
+    one_way
+  end
+
+  def genome_from_fname fname
+    fname_no_aai = fname.split(BLAST_DB_SEPARATOR).first
+    ext = fname_no_aai.split(".").last
+    genome = File.basename fname_no_aai, ".#{ext}"
+
+    genome
+  end
+
+  def clean_header header
+    header.gsub(/ +/, "_")
+  end
+
+  # Adds the file name to the header minus the directory and the
+  # final extension.
+  #
+  # @note If the file is blah.fa.gz or something like that, then the
+  #   genome name will be blah.fa, and not just blah.
+  def annotate_header header, fname
+    genome = genome_from_fname fname
+
+    "#{genome}____#{header}"
+  end
+end

data/lib/aai/core_extensions.rb

@@ -0,0 +1,80 @@
+module Aai
+  module CoreExtensions
+    module Time
+      def date_and_time fmt="%F %T.%L"
+        Object::Time.now.strftime fmt
+      end
+
+      def time_it title="", logger=nil, run: true
+        if run
+          t = Object::Time.now
+
+          yield
+
+          time = Object::Time.now - t
+
+          if title == ""
+            msg = "Finished in #{time} seconds"
+          else
+            msg = "#{title} finished in #{time} seconds"
+          end
+
+          if logger
+            logger.info msg
+          else
+            $stderr.puts msg
+          end
+        end
+      end
+    end
+
+    module Process
+      include CoreExtensions::Time
+
+      def run_it *a, &b
+        exit_status, stdout, stderr = systemu *a, &b
+
+        puts stdout unless stdout.empty?
+        $stderr.puts stderr unless stderr.empty?
+
+        exit_status.exitstatus
+      end
+
+      def run_it! *a, &b
+        exit_status = self.run_it *a, &b
+
+        AbortIf.abort_unless exit_status.zero?,
+                             "ERROR: non-zero exit status " +
+                             "(#{exit_status}) " +
+                             "when running '#{a.inspect}', " +
+                             "'#{b.inspect}'"
+
+        exit_status
+      end
+
+      # Examples
+      #
+      # Process.extend CoreExtensions::Process
+      # Time.extend CoreExtensions::Time
+      #
+      # Process.run_and_time_it! "Saying hello",
+      #                          %Q{echo "hello world"}
+      #
+      # Process.run_and_time_it! "This will raise SystemExit",
+      #                          "ls arstoeiarntoairnt" do
+      #   puts "i like pie"
+      # end
+      def run_and_time_it! title="",
+                           cmd="",
+                           logger=AbortIf::logger,
+                           &b
+
+        AbortIf.logger.debug { "Running: #{cmd}" }
+
+        time_it title, logger do
+          run_it! cmd, &b
+        end
+      end
+    end
+  end
+end

data/lib/aai/utils.rb

@@ -0,0 +1,36 @@
+module Aai
+  module Utils
+    # Raises SystemExit if one of the fnames does not exist.
+    def check_files fnames
+      fnames.each do |fname|
+        AbortIf.abort_unless_file_exists fname
+      end
+    end
+
+    def two_ary_permutations a1, a2
+      permutations = []
+
+      a1.each do |elem1|
+        a2.each do |elem2|
+          permutations << [elem1, elem2] << [elem2, elem1]
+        end
+      end
+
+      permutations
+    end
+
+    def one_way_combinations a1, a2, no_duplicates=true
+      permutations = []
+
+      a1.each do |elem1|
+        a2.each do |elem2|
+          if !no_duplicates || (no_duplicates && elem1 != elem2)
+            permutations << [elem1, elem2]
+          end
+        end
+      end
+
+      permutations
+    end
+  end
+end

data/lib/aai/version.rb

@@ -0,0 +1,13 @@
+module Aai
+  VERSION = "0.1.0"
+  COPYRIGHT = "2017 Ryan Moore"
+  CONTACT   = "moorer@udel.edu"
+  WEBSITE   = "https://github.com/mooreryan/aai"
+  LICENSE   = "MIT"
+
+  VERSION_BANNER = "  # Version: #{VERSION}
+  # Copyright #{COPYRIGHT}
+  # Contact: #{CONTACT}
+  # Website: #{WEBSITE}
+  # License: #{LICENSE}"
+end

metadata

@@ -0,0 +1,200 @@
+--- !ruby/object:Gem::Specification
+name: aai
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Ryan Moore
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-06-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.21
+- !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: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+- !ruby/object:Gem::Dependency
+  name: abort_if
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: parse_fasta
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.2'
+- !ruby/object:Gem::Dependency
+  name: systemu
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.6.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.6.5
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.1.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.1.2
+description: Calculate Seanie's amino acid similarity score between multiple genomes/bins.
+email:
+- moorer@udel.edu
+executables:
+- aai.rb
+extensions: []
+extra_rdoc_files: []
+files:
+- ".coveralls.yml"
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- aai.gemspec
+- bin/console
+- bin/setup
+- exe/aai.rb
+- lib/aai.rb
+- lib/aai/core_extensions.rb
+- lib/aai/utils.rb
+- lib/aai/version.rb
+homepage: https://github.com/mooreryan/aai.git
+licenses:
+- MIT
+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: 2.6.12
+signing_key: 
+specification_version: 4
+summary: Seanie's amino acid similarity.
+test_files: []