matr 0.0.1 → 0.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -0,0 +1,37 @@
+PATH
+  remote: .
+  specs:
+    matr (0.0.1)
+      trollop (~> 2.1, >= 2.1.3)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    diff-lcs (1.3)
+    rake (10.5.0)
+    rspec (3.8.0)
+      rspec-core (~> 3.8.0)
+      rspec-expectations (~> 3.8.0)
+      rspec-mocks (~> 3.8.0)
+    rspec-core (3.8.0)
+      rspec-support (~> 3.8.0)
+    rspec-expectations (3.8.1)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-mocks (3.8.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-support (3.8.0)
+    trollop (2.1.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.16)
+  matr!
+  rake (~> 10.0)
+  rspec (~> 3.0)
+
+BUNDLED WITH
+   1.16.4

data/README.md

@@ -16,10 +16,6 @@ Or install it yourself as:
 
     $ gem install matr
 
-## 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.

data/exe/matr

@@ -0,0 +1,98 @@
+#!/usr/bin/env ruby
+
+Signal.trap("PIPE", "EXIT")
+
+require "set"
+require "trollop"
+
+opts = Trollop.options do
+  banner <<-EOS
+
+  Take a three-column matrix file and ensure that it is symmetric for input into R.
+
+  Options:
+  EOS
+
+  opt(:infile, "Input file", type: :string)
+
+  opt(:self_score, "Score for self connections", default: 100)
+  opt(:missing_score, "Score for missing connections", default: 0)
+  opt(:output_style, "Output style [wide,long]", default: "wide")
+end
+
+infile = opts[:infile]
+self_score = opts[:self_score]
+missing_score = opts[:missing_score]
+output_style = opts[:output_style]
+
+unless File.exist? infile
+  abort "FATAL -- infile '#{infile}' does not exist"
+end
+
+unless output_style == "wide" || output_style == "long"
+  abort "FATAL -- output style must be either wide or long"
+end
+
+graph = Hash.new { |ht, k| ht[k] = Hash.new }
+all_keys = Set.new
+header   = nil
+
+File.open(infile, "rt").each_line.with_index do |line, idx|
+  line.chomp!
+
+  if idx.zero?
+    header = line
+  else
+    source, target, score = line.split "\t"
+
+    all_keys << source << target
+
+    # If you have duplicates with different scores, that's an error: a
+    # => b = 10 and a => b = 20
+    if graph[source].has_key?(target) && graph[source][target] != score
+      abort "source--target (#{source}--#{target}) was repeated with a different score"
+    end
+
+    graph[source][target] = score
+
+    # Since you might have a files that specifies a => b = 10, and b
+    # => a = 10, that would be okay.  But if you have a => b = 10, and
+    # b => a = 5, then that would be an error.
+    if graph[target].has_key?(source) && graph[target][source] != score
+      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."
+
+    end
+
+    graph[target][source] = score
+
+    unless graph[target].has_key? target
+      graph[target][target] = self_score
+    end
+
+    unless graph[source].has_key? source
+      graph[source][source] = self_score
+    end
+  end
+end
+
+if output_style == "long"
+  puts header
+
+  all_keys.each do |source|
+    all_keys.each do |target|
+      puts [source, target, graph[source][target] || missing_score].join "\t"
+    end
+  end
+else
+  all_keys = all_keys.sort
+
+  puts ["", all_keys].join "\t"
+
+  all_keys.each do |source|
+    row = all_keys.map do |target|
+      graph[source][target] || missing_score
+    end
+
+    puts [source, row].join "\t"
+  end
+end

data/lib/matr/version.rb

@@ -1,3 +1,3 @@
 module Matr
-  VERSION = "0.0.1"
+  VERSION = "0.0.2"
 end

data/matr.gemspec

@@ -22,6 +22,8 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
+  spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.3"
+
   spec.add_development_dependency "bundler", "~> 1.16"
   spec.add_development_dependency "rake", "~> 10.0"
   spec.add_development_dependency "rspec", "~> 3.0"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: matr
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Ryan Moore
@@ -10,6 +10,26 @@ bindir: exe
 cert_chain: []
 date: 2018-08-23 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.1.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.1.3
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -55,7 +75,8 @@ dependencies:
 description: Deal text file matrices.
 email:
 - moorer@udel.edu
-executables: []
+executables:
+- matr
 extensions: []
 extra_rdoc_files: []
 files:
@@ -64,11 +85,13 @@ files:
 - ".travis.yml"
 - CODE_OF_CONDUCT.md
 - Gemfile
+- Gemfile.lock
 - LICENSE.txt
 - README.md
 - Rakefile
 - bin/console
 - bin/setup
+- exe/matr
 - lib/matr.rb
 - lib/matr/version.rb
 - matr.gemspec