transrate 0.0.16 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 11e11ad4e926162c2f5abf2a77c77be603dee85a
-  data.tar.gz: cd9d544e1ab00d43314bba1b3fcebf2fb9cac2f9
+  metadata.gz: cfac9099c06f657ebaa995763f287339e1527a5d
+  data.tar.gz: 5281dc92d37cccc7f518622c223ffcbdeef86fff
 SHA512:
-  metadata.gz: 39385d5c1e6badec90cfc732cd50daa78a38fb7756ccd97223dfcc512de2445c04cdb03c79910e367c2f141653d33a298325d67565e13d4ee5b0fde0a424ae66
-  data.tar.gz: 75b91afe62981e0b71e16fb9e80325ba7950f44d2b81716565d123bef591085f3b273d44d1ed75882b25533724ae2e6a86efa3c500a0c3f3ee96bf3efa9ef13e
+  metadata.gz: 56715785fb5dd0f8f50cae0092d35cb5ef38c80a84c4f9575cac936f520056fac3e5c626a56d07b83bcaf12d5827472d8ca6378b33bed4efd4fcebc12a122a4c
+  data.tar.gz: 032e000796a0df849f2650cf861c9a5756272c0cde7fb8ffd3ba0a31117e003c5806a717f10fcc021947048ba12578ae8016ad6944f0b5f22953a899c5d88198

data/bin/transrate

@@ -141,14 +141,17 @@ opts.assembly.split(',').each do |assembly|
     end
 
     log "Comparative metrics done in #{Time.now - t0} seconds"
-  end
 
-  log "\n"
-  log "-" * report_width
-  score = transrater.assembly_score
-  unless score.nil?
-    log "OVERALL SCORE: #{score.to_f.round(2) * 100}%"
+
+    log "\n"
     log "-" * report_width
+    score = transrater.assembly_score
+    unless score.nil?
+      log "OVERALL SCORE: #{score.to_f.round(2) * 100}%"
+      log "-" * report_width
+    end
+  else
+    log "\nNo reference provided, skipping comparative diagnostics"
   end
 
   all << contig_results.

data/lib/transrate/assembly.rb

@@ -87,6 +87,9 @@ module Transrate
     # @return [Hash] basic statistics about the assembly
     def basic_stats threads=8
       
+      # disable threading basic stats for now
+      threads = 1
+
       # create a work queue to process contigs in parallel
       queue = Queue.new
       
@@ -167,10 +170,10 @@ module Transrate
       # the next value to set the next cutoff. we take a copy
       # of the Array so we can use the intact original to collect
       # the results later
-      # x = [90, 70, 50, 30, 10]
-      # x2 = x.clone
-      # cutoff = x2.pop / 100.0
-      # res = []
+      x = [90, 70, 50, 30, 10]
+      x2 = x.clone
+      cutoff = x2.pop / 100.0
+      res = []
       n1k = 0
       n10k = 0
       orf_length_sum = 0
@@ -193,19 +196,20 @@ module Transrate
         # cutoff has been reached. if it has, store the Nx value and
         # get the next cutoff
         cumulative_length += contig.length
-#        if cumulative_length >= @n_bases * cutoff
-#          res << contig.length
-#          if x2.empty?
-#            cutoff=1
-#          else
-#            cutoff = x2.pop / 100.0
-#          end 
-#        end
+        if cumulative_length >= @n_bases * cutoff
+          res << contig.length
+          if x2.empty?
+            cutoff=1
+          else
+            cutoff = x2.pop / 100.0
+          end 
+        end
+
       end
 
       # calculate and return the statistics as a hash
       mean = cumulative_length / @assembly.size
- #     ns = Hash[x.map { |n| "N#{n}" }.zip(res)]
+      ns = Hash[x.map { |n| "N#{n}" }.zip(res)]
       {
         'n_seqs' => bin.size,
         'smallest' => bin.first.length,
@@ -215,8 +219,7 @@ module Transrate
         'n_1k' => n1k,
         'n_10k' => n10k,
         'orf_percent' => 300 * orf_length_sum / (@assembly.size * mean)
-      }
-#      }.merge ns
+      }.merge ns
 
     end # basic_bin_stats
 

data/lib/transrate/transrater.rb

@@ -24,7 +24,9 @@ module Transrate
     # @param insertsd [Integer] standard deviation of the read pair insert size
     def initialize assembly, reference, left=nil, right=nil, insertsize=nil, insertsd=nil
       @assembly  = assembly.is_a?(Assembly)  ? assembly  : Assembly.new(assembly)
-      @reference = reference.is_a?(Assembly) ? reference : Assembly.new(reference)
+      if reference
+        @reference = reference.is_a?(Assembly) ? reference : Assembly.new(reference)
+      end
       @read_metrics = ReadMetrics.new @assembly
       @comparative_metrics = ComparativeMetrics.new(@assembly, @reference)
     end

data/lib/transrate/version.rb

@@ -9,8 +9,8 @@ module Transrate
   # Semantic Versioning 2.0 (http://semver.org/).
   module VERSION
     MAJOR = 0
-    MINOR = 0
-    PATCH = 16
+    MINOR = 1
+    PATCH = 0
     BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 0.0.16
+  version: 0.1.0
 platform: ruby
 authors:
 - Richard Smith