MSAbundanceSim 0.2.0 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 268fcffc387bab3d7171a689587d31608f310caa
-  data.tar.gz: c96eec4ada2a66919d2cb169386dedd67b3ecaf6
+  metadata.gz: 15ce22fdc00a43ccd1de3e549b7686ce1163b640
+  data.tar.gz: 25bf60003d8eccaa9d02a7173528d7a58d58bddc
 SHA512:
-  metadata.gz: f04254780acc303a1740e788e55f4e29293f46e38f4a1a1f65d9718019485602d47de1ed20e506c0db7f35c87a67ba216a3b8f1cea04a7f952f456b289f53b60
-  data.tar.gz: edc6f893102eedcef87ba5e413dfd7dc1abc7ac3b99ee598b9d94dddab5cc67164c6ad351fed1fa26223d235ebb8e511124bce727612359f83f922a2834a96b8
+  metadata.gz: f0e0e2327e26353dd960bd3986d958e397ade85c7145ba556abe7109bae38d9f21b16ec51b04b4e701d3ed9e24c8a90b56358cb8e002dc81e8d21737806de54d
+  data.tar.gz: 9ad8473d36030038fb20b2f94c1c39d0167fbb11ffbebc7e4e9f61bb4eb3d9cdc10ff863074e18e3448afb30128e78cc9c3e865fd745e60a85fc855ee2242f03

data/lib/ms_abundance_sim.rb

@@ -9,7 +9,7 @@ require 'set'
 require 'yaml'
 
 class MSAbundanceSim
-  VERSION = "0.2.0"
+  VERSION = "0.3.0"
 end
 
 ProteinEntry = Struct.new(:entry_line_wo_abundance, :abundances, :additional_lines) do
@@ -34,9 +34,8 @@ class MSAbundanceSim
     control_variance: 1,
     case_variance: 2,
     output_abundance_separator: " #",
-    downshift_min_threshold: 0,
+    downshift_min_threshold: 1.0,
     downshift_probability_threshold: 0.75,
-    downshift_amount: 1,
   }
 
   class << self
@@ -77,12 +76,13 @@ class MSAbundanceSim
       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
+    # takes 'value' and subtracts rand(min_threshold..value) from it if
+    # 'value' is >= 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, random=rand())
+      if (value >= min_threshold) && (random < probability_threshold)
+        value - rand(min_threshold..value)
       else
         value
       end
@@ -136,7 +136,7 @@ class MSAbundanceSim
 
           fold_change = MSAbundanceSim.get_fold_change(protein_entry.abundances, variance, max_abundance)
 
-          downshift_params = %w(min_threshold probability_threshold amount)
+          downshift_params = %w(min_threshold probability_threshold)
             .map {|key| 'downshift_' + key }
             .map(&:to_sym)
             .map {|key| opts[key] }
@@ -279,14 +279,6 @@ class MSAbundanceSim
             "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]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: MSAbundanceSim
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors:
 - Rob Smith, John T. Prince
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-05-18 00:00:00.000000000 Z
+date: 2017-05-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler