matr 0.0.1 → 0.0.2
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- checksums.yaml +4 -4
- data/Gemfile.lock +37 -0
- data/README.md +0 -4
- data/exe/matr +98 -0
- data/lib/matr/version.rb +1 -1
- data/matr.gemspec +2 -0
- metadata +25 -2
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0aefd54bc8a7c57da41e3843bbc8cd9e29885457
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data.tar.gz: 3f6a1f167731135a93423bcb076a99259a22a5de
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 47c0ca490761b79d628b72ba7ae805450844da7ec550284207fe4cea78e497cf239f71faf9ee5de070b319e9137bd869997c3776bd3d764db0ecf5a01f722326
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data.tar.gz: 0baeb31d028459fba8ab48a409e3f5666c1c3d4449504b92e32d233b5291acf3288801404d628d36acedccc4657cdebb1a3cbf4000a608bec0d74d7bcfa074ea
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data/Gemfile.lock
ADDED
@@ -0,0 +1,37 @@
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1
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PATH
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remote: .
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specs:
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matr (0.0.1)
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5
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trollop (~> 2.1, >= 2.1.3)
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7
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GEM
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remote: https://rubygems.org/
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specs:
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10
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diff-lcs (1.3)
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rake (10.5.0)
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rspec (3.8.0)
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rspec-core (~> 3.8.0)
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rspec-expectations (~> 3.8.0)
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rspec-mocks (~> 3.8.0)
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rspec-core (3.8.0)
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rspec-support (~> 3.8.0)
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rspec-expectations (3.8.1)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.8.0)
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rspec-mocks (3.8.0)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.8.0)
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rspec-support (3.8.0)
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trollop (2.1.3)
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PLATFORMS
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ruby
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30
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DEPENDENCIES
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bundler (~> 1.16)
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32
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matr!
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rake (~> 10.0)
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34
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rspec (~> 3.0)
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35
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BUNDLED WITH
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1.16.4
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data/README.md
CHANGED
@@ -16,10 +16,6 @@ Or install it yourself as:
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$ gem install matr
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-
## Usage
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-
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TODO: Write usage instructions here
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-
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## Development
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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.
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data/exe/matr
ADDED
@@ -0,0 +1,98 @@
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1
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#!/usr/bin/env ruby
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2
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Signal.trap("PIPE", "EXIT")
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4
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require "set"
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6
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require "trollop"
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7
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8
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opts = Trollop.options do
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9
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banner <<-EOS
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10
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11
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Take a three-column matrix file and ensure that it is symmetric for input into R.
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Options:
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EOS
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15
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opt(:infile, "Input file", type: :string)
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opt(:self_score, "Score for self connections", default: 100)
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19
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opt(:missing_score, "Score for missing connections", default: 0)
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20
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opt(:output_style, "Output style [wide,long]", default: "wide")
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21
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end
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infile = opts[:infile]
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self_score = opts[:self_score]
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missing_score = opts[:missing_score]
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output_style = opts[:output_style]
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27
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unless File.exist? infile
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29
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abort "FATAL -- infile '#{infile}' does not exist"
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30
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end
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31
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+
|
32
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unless output_style == "wide" || output_style == "long"
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abort "FATAL -- output style must be either wide or long"
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end
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36
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graph = Hash.new { |ht, k| ht[k] = Hash.new }
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all_keys = Set.new
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header = nil
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40
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File.open(infile, "rt").each_line.with_index do |line, idx|
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line.chomp!
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42
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43
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if idx.zero?
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44
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header = line
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45
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else
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46
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source, target, score = line.split "\t"
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47
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|
48
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all_keys << source << target
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49
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|
50
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# If you have duplicates with different scores, that's an error: a
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51
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# => b = 10 and a => b = 20
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52
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if graph[source].has_key?(target) && graph[source][target] != score
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abort "source--target (#{source}--#{target}) was repeated with a different score"
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54
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end
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|
56
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graph[source][target] = score
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57
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58
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# Since you might have a files that specifies a => b = 10, and b
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59
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# => a = 10, that would be okay. But if you have a => b = 10, and
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# b => a = 5, then that would be an error.
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61
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if graph[target].has_key?(source) && graph[target][source] != score
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abort "target--source (#{target}--#{source}) is specified seperately from source--target (#{source}--#{target}), BUT there scores do not match. This means your matrix is NOT symmetric."
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end
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65
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|
66
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graph[target][source] = score
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67
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68
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unless graph[target].has_key? target
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graph[target][target] = self_score
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end
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71
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unless graph[source].has_key? source
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graph[source][source] = self_score
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end
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end
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end
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if output_style == "long"
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puts header
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all_keys.each do |source|
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all_keys.each do |target|
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puts [source, target, graph[source][target] || missing_score].join "\t"
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84
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end
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85
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end
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else
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all_keys = all_keys.sort
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88
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89
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puts ["", all_keys].join "\t"
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91
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all_keys.each do |source|
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row = all_keys.map do |target|
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graph[source][target] || missing_score
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end
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95
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96
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puts [source, row].join "\t"
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97
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end
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98
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end
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data/lib/matr/version.rb
CHANGED
data/matr.gemspec
CHANGED
@@ -22,6 +22,8 @@ Gem::Specification.new do |spec|
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spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
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spec.require_paths = ["lib"]
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spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.3"
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spec.add_development_dependency "bundler", "~> 1.16"
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spec.add_development_dependency "rake", "~> 10.0"
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spec.add_development_dependency "rspec", "~> 3.0"
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: matr
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3
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version: !ruby/object:Gem::Version
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version: 0.0.
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version: 0.0.2
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platform: ruby
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authors:
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- Ryan Moore
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@@ -10,6 +10,26 @@ bindir: exe
|
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cert_chain: []
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date: 2018-08-23 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: trollop
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.1'
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- - ">="
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- !ruby/object:Gem::Version
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version: 2.1.3
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.1'
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- - ">="
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- !ruby/object:Gem::Version
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version: 2.1.3
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- !ruby/object:Gem::Dependency
|
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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@@ -55,7 +75,8 @@ dependencies:
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description: Deal text file matrices.
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email:
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- moorer@udel.edu
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executables:
|
78
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executables:
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- matr
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extensions: []
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extra_rdoc_files: []
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files:
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@@ -64,11 +85,13 @@ files:
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- ".travis.yml"
|
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- CODE_OF_CONDUCT.md
|
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87
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- Gemfile
|
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- Gemfile.lock
|
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- LICENSE.txt
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- README.md
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- Rakefile
|
70
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- bin/console
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- bin/setup
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- exe/matr
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95
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- lib/matr.rb
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96
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- lib/matr/version.rb
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- matr.gemspec
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