sequences.rb in genomer-plugin-summary-0.0.3

- old
+ new

@@ -1,9 +1,11 @@
 require 'genomer'
+require 'genomer-plugin-summary/metrics'
 require 'terminal-table'
 
 class GenomerPluginSummary::Sequences < Genomer::Plugin
+  include GenomerPluginSummary::Metrics
 
   def run
     sequences = calculate(scaffold)
     total     = total(sequences)
 
@@ -49,26 +51,26 @@
       map{|i| hash[i]}.
       map{|i| i.class == Float ? sprintf('%#.2f',i) : i }
   end
 
   def calculate(scaffold)
-    total_length = scaffold.map(&:sequence).join.length.to_f
+    total_length   = length(:all,scaffold).to_f
+    running_length = 0
 
-    length = 0
     scaffold.map do |entry|
       i = nil
       if entry.entry_type != :unresolved
         entry_length = entry.sequence.length
         i = { :sequence => entry.source,
-              :start    => length + 1, 
-              :end      => length + entry_length,
+              :start    => running_length + 1,
+              :end      => running_length + entry_length,
               :size     => entry_length,
               :percent  => entry_length / total_length * 100,
-              :gc       => gc_content(entry.sequence) }
+              :gc       => gc(entry) / atgc(entry) * 100 }
       end
         
-      length += entry.sequence.length
+      running_length += entry.sequence.length
       i
     end.compact
   end
 
   def total(seqs)
@@ -83,13 +85,8 @@
 
       hash
     end
     totals[:gc] /= totals[:size]
     totals
-  end
-
-  def gc_content(sequence)
-    nucleotides = sequence.gsub(/[^ATGCatgc]/,'')
-    nucleotides.gsub(/[^GCgc]/,'').length.to_f / nucleotides.length * 100
   end
 
 end