matr 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/exe/matr

@@ -7,38 +7,93 @@ require "matr"
 require "set"
 require "trollop"
 
+mode_info = <<-EOS
+  Modes
+  -----
+
+    - All vs. all non-symmetric (ava): I will make a square matrix
+      that contains all versus all comparisons for each item
+      specified, regardless of the column that the item was in.  Any
+      comparisons not specified in the input file will get an 'na'
+      value (or whatever you tell us to replace it with).
+
+    - All vs. all symmetric (ava_symmetric): I will also ensure
+      symmetry by adding a reverse entry for each row (i.e., source -
+      target - score AND target - source - score), even if the reverse
+      entry isn't specified explicitly.  If this isn't possible, then
+      I will raise an error.
+EOS
+
 opts = Trollop.options do
   banner <<-EOS
 
-  Take a three-column matrix file and ensure that it is symmetric for input into R.
+  Take a three-column matrix file and do stuff with it.
+
 
-  *Note* -- I ALWAYS enforce symmetry of the output.
+#{mode_info}
 
   Option details
   --------------
 
-  --self-scores: I will add a self score of this value if one is not already specified.
-  --ensure-self-scores: I will ensure all self scores equal the value set in --self-scores even if a self-score is present but set to something else.
+    --self-scores: I will add a self score of this value if one is not
+      already specified.
 
-  Things I do
-  ------------------
+    --ensure-self-scores: I will ensure all self scores equal the
+      value set in --self-scores even if a self-score is present but
+      set to something else.
+
+    --na-replace <value>: If you pass this flag, I will replace any
+      'na' values with this value.
 
-    - Raise error if a source-target pair is specified twice with a different score
-    - Raise error if source-target and target-source are both specified and they don't match.
 
   Options:
   EOS
 
-  opt(:infile, "Input file", type: :string)
+  opt(:infile,
+      "Input file",
+      type: :string)
+
+  opt(:mode,
+      "Which mode should I run in?",
+      default: "ava")
+  opt(:print_modes,
+      "Print available modes then exit")
+
+  opt(:na_replace,
+      "Replace any 'na' values with this value",
+      default: 0)
+
+  opt(:self_score,
+      "Score for self connections",
+      default: 100)
+  opt(:ensure_self_scores,
+      "This flag will ensure that self hit scores all match the " \
+      "value of --self-score option")
+
+  opt(:output_style,
+      "Output style [wide,long]",
+      default: "wide")
+end
+
+if opts[:print_modes]
+  help = <<-EOS
 
-  opt(:missing_score, "Score for missing connections (unless they are already put in because of symmetry)", default: 0)
+  Available modes: ava, ava_symmetric
 
-  # opt(:ensure_symmetry, "This flag will ensure that your output will be a symmetric matrix.", default: true)
+#{mode_info}
+  EOS
 
-  opt(:self_score, "Score for self connections", default: 100)
-  opt(:ensure_self_scores, "This flag will ensure that self hit scores all match the value of --self-score option", default: true)
+  STDERR.puts help
+  exit
+end
 
-  opt(:output_style, "Output style [wide,long]", default: "wide")
+unless opts[:infile_given]
+  abort "FATAL: --infile is a required argument"
 end
 
-Matr.main opts
+begin
+  Matr.main opts
+rescue StandardError => err
+  # We only are meant to throw StandardError
+  abort err
+end

data/lib/matr.rb

@@ -8,12 +8,18 @@ module Matr
   def self.main opts
 
     infile             = opts[:infile]
+    mode               = self.default_opt opts, :mode, "ava"
     self_score         = self.default_opt opts, :self_score, 100
-    missing_score      = self.default_opt opts, :missing_score, 0
-    output_style       = self.default_opt opts, :output_style, "wide"
-    ensure_symmetry    = true # self.default_opt opts, :ensure_symmetry, true
     ensure_self_scores = self.default_opt opts, :ensure_self_scores, true
 
+    if opts[:na_replace_given]
+      missing_score = opts[:na_replace]
+    else
+      missing_score = "na"
+    end
+
+    output_style = self.default_opt opts, :output_style, "wide"
+
     unless File.exist? infile
       raise StandardError, "FATAL -- infile '#{infile}' does not exist"
     end
@@ -36,20 +42,15 @@ module Matr
 
         all_keys << source << target
 
-        # Fix self score if the option is there.
-        if source == target && ensure_self_scores
-          score = self_score
-        end
-
         # 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
-          raise StandardError, "FATAL -- source--target (#{source}--#{target}) was repeated with a different score"
+          raise StandardError, "FATAL -- source--target (#{source}--#{target}) was repeated with a different score.  Old score was #{graph[source][target]}, and the new score was #{score}."
         end
 
         graph[source][target] = score
 
-        if ensure_symmetry
+        if mode == "ava_symmetric"
           # 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.
@@ -59,14 +60,17 @@ module Matr
 
           graph[target][source] = score
         end
+      end
+    end
 
-        # Makes sure these weren't already specified earlier.
-        unless graph[target].has_key? target
-          graph[target][target] = self_score
-        end
+    all_keys = all_keys.to_a.sort
 
-        unless graph[source].has_key? source
-          graph[source][source] = self_score
+    # Zip through and add any self scores that weren't added.
+    all_keys.each do |source|
+      all_keys.each do |target|
+        # With ensure_self_scores, we overwrite the self score even if it was already given.  Otherwise, only if it was NOT given.
+        if source == target && (ensure_self_scores || !graph[source][target])
+          graph[source][target] = self_score
         end
       end
     end
@@ -80,8 +84,6 @@ module Matr
         end
       end
     else
-      all_keys = all_keys.sort
-
       puts ["", all_keys].join "\t"
 
       all_keys.each do |source|

data/lib/matr/version.rb

@@ -1,3 +1,3 @@
 module Matr
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: matr
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2018-08-24 00:00:00.000000000 Z
+date: 2018-08-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop