transrate 0.0.7 → 0.0.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: dfc72856627c9ac051379efaf1bd8e835851b16f
-  data.tar.gz: cdd22a20b948adf89cb7707ceac2789a944f29a6
+  metadata.gz: ad3086d63ee5deaf6ed931c5df095e776e601e2e
+  data.tar.gz: 188ff6eb56896b42de4ec8e4cee31e23d8387bed
 SHA512:
-  metadata.gz: 0ec91bfbb2991f784340b0df5fedb88bc4f009d5a51c2365ebd50bf8b573bbaedcd8cb2c7e516ca7281a8c00b807f6191834d3c58150aa0d6d9d8304e8fe57de
-  data.tar.gz: 1aa48ef3d32ec27a17d25ecb586a4eca2085d2e1dc9499c8709fdd729d1902321d371fb0dd68a858da6989eb811195a914affbace3ea95533a4f008a698f58a2
+  metadata.gz: 949dd128cb648f481bd7f473e037d9873325407393981674888b04e1b07f9729a1da5cd9d1efb42fb55838cfabcd6c03e33b42b9cfd25f80168fe78175aac035
+  data.tar.gz: 985cdfc7335410d3c7bd7f1c086b8d0aa87bd66b3af6e8859cc86d000583cca4b8dd728fce76add4e37b14636cd30a04d1876181a3879ec473a11f58368aaa69

data/.gitignore

@@ -17,3 +17,4 @@ tmp
 .yardoc
 _yardoc
 doc/
+.ruby-version

data/lib/transrate/assembly.rb

@@ -83,8 +83,8 @@ module Transrate
         "largest" => @assembly.last.length,
         "n_bases" => @n_bases,
         "mean_len" => mean,
-        "n > 1k" => n1k,
-        "n > 10k" => n10k
+        "n_1k" => n1k,
+        "n_10k" => n10k
       }.merge ns
     end
 

data/lib/transrate/comparative_metrics.rb

@@ -15,7 +15,7 @@ module Transrate
     def run
       rbu = self.reciprocal_best_ublast
       @ortholog_hit_ratio = self.ortholog_hit_ratio rbu
-      @collapse_factor = self.collapse_factor @ra.l2r_hits
+      @collapse_factor = self.collapse_factor @ra.r2l_hits
       @reciprocal_hits = rbu.size
       {
         :reciprocal_hits => @reciprocal_hits,
@@ -29,23 +29,26 @@ module Transrate
       @ra.run
     end
 
-    def ortholog_hit_ratio rbu
+    def ortholog_hit_ratio rbu=nil
       return @ortholog_hit_ratio unless @ortholog_hit_ratio.nil? 
       rbu.reduce(0.0){ |sum, hit| sum += hit.last.tcov.to_f } / rbu.size
     end
 
-    def collapse_factor hits
+    def collapse_factor hits=nil
       return @collapse_factor unless @collapse_factor.nil?
       targets = {}
       hits.each_pair do |query, hit|
-        unless targets.has_key? query
-          targets[query] = Set.new
+        target = hit.target
+        unless targets.has_key? target 
+          targets[target] = Set.new
         end
-        targets[query] << hit.target
+        targets[target] << query
       end
-      targets.values.reduce(0.0){ |sum, val| sum += val.size } / targets.size
+      sum = targets.values.reduce(0.0){ |sum, val| sum += val.size }
+      puts "sum: #{sum}"
+      sum / targets.size
     end
 
   end # ComparativeMetrics
 
-end # Transrate
+end # Transrate

data/lib/transrate/read_metrics.rb

@@ -2,6 +2,7 @@ module Transrate
 
   class ReadMetrics
 
+    attr_reader :total
     attr_reader :bad
     attr_reader :supported_bridges
 
@@ -17,9 +18,14 @@ module Transrate
                                   left, right, 
                                   insertsize, insertsd)
       self.analyse_read_mappings(samfile, insertsize, insertsd)
+      @percent_mapping = @total.to_f / @num_pairs.to_f * 100.0
+      @pc_good_mapping = @good.to_f / @num_pairs.to_f * 100.0
       {
+        :num_pairs => @num_pairs,
         :total_mappings => @total,
+        :percent_mapping => @percent_mapping,
         :good_mappings => @good,
+        :pc_good_mapping => @pc_good_mapping,
         :bad_mappings => @bad,
         :both_mapped => @both_mapped,
         :properly_paired => @properly_paired,
@@ -54,6 +60,7 @@ module Transrate
     end
 
     def initial_values
+      @num_pairs = 100000
       @total = 0
       @good = 0
       @bad = 0
@@ -158,4 +165,4 @@ module Transrate
 
   end # ReadMetrics
 
-end # Transrate
+end # Transrate

data/lib/transrate/transrater.rb

@@ -2,6 +2,10 @@ module Transrate
 
   class Transrater
 
+    attr_reader :assembly
+    attr_reader :read_metrics
+    attr_reader :comparative_metrics
+
     def initialize assembly, reference, left, right, insertsize=nil, insertsd=nil
       @assembly = Assembly.new assembly
       @reference = reference.is_a?(Assembly) ? reference : Assembly.new(reference)
@@ -18,4 +22,4 @@ module Transrate
 
   end # Transrater
 
-end # Transrate
+end # Transrate

data/lib/transrate/version.rb

@@ -4,7 +4,7 @@ module Transrate
   module VERSION
     MAJOR = 0
     MINOR = 0
-    PATCH = 7
+    PATCH = 8
     BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')

data/transrate.gemspec

@@ -6,6 +6,7 @@ Gem::Specification.new do |gem|
   gem.name          = 'transrate'
   gem.authors       = [ "Richard Smith" ]
   gem.email         = "rds45@cam.ac.uk"
+  gem.licenses      = ["MIT"]
   gem.homepage      = 'https://github.com/blahah/assemblotron'
   gem.summary       = %q{ quality assessment of de-novo transcriptome assemblies }
   gem.description   = %q{ a library and command-line tool for quality assessment of de-novo transcriptome assemblies }
@@ -25,4 +26,4 @@ Gem::Specification.new do |gem|
   gem.add_development_dependency 'simplecov'
   gem.add_development_dependency 'shoulda-context'
   gem.add_development_dependency 'coveralls', '~> 0.6.7'
-end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.8
 platform: ruby
 authors:
 - Richard Smith
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-19 00:00:00.000000000 Z
+date: 2013-09-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -146,7 +146,6 @@ extra_rdoc_files: []
 files:
 - .gitignore
 - Gemfile
-- Gemfile.lock
 - LICENSE
 - README.md
 - bin/transrate
@@ -162,7 +161,8 @@ files:
 - lib/transrate/version.rb
 - transrate.gemspec
 homepage: https://github.com/blahah/assemblotron
-licenses: []
+licenses:
+- MIT
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -180,7 +180,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.1.4
 signing_key: 
 specification_version: 4
 summary: quality assessment of de-novo transcriptome assemblies