lib/seqtrimnext/classes/extract_stats.rb in seqtrimnext-2.0.51 vs lib/seqtrimnext/classes/extract_stats.rb in seqtrimnext-2.0.52

@@ -9,24 +9,24 @@
 require 'scbi_plot'
 require "scbi_math"
 
 class ExtractStats
 
-  def initialize(sequence_reader,params)
+  def initialize(sequence_readers,params)
 
     @sequence_lengths = []         #array of sequences lengths
     @length_frequency = []      #number of sequences of each size (frequency)
     @keys={}  #found keys
     @params = params
-    @use_qual=sequence_reader.with_qual?
+    @use_qual=sequence_readers.first.with_qual?
     # @params.get_param('use_qual')
 
     @totalnt=0
     @qv=[]
 
 
-    @sequence_lengths_stats, @length_frequency_stats, @quality_stats = extract_stats_from_sequences(sequence_reader)
+    @sequence_lengths_stats, @length_frequency_stats, @quality_stats = extract_stats_from_sequences(sequence_readers)
 
 
     set_params_and_results
 
     plot_lengths
@@ -35,34 +35,37 @@
 
     print_global_stats
 
   end
 
-  def extract_stats_from_sequences(sequence_reader)
+  def extract_stats_from_sequences(sequence_readers)
+    sequence_readers.each do |sequence_reader|
 
-    sequence_reader.each do |name_seq,fasta_seq,qual|
-      l = fasta_seq.length
 
-      @totalnt+=l
+      sequence_reader.each do |name_seq,fasta_seq,qual|
+        l = fasta_seq.length
 
-      #save all lengths
-      @sequence_lengths.push l
+        @totalnt+=l
 
-      # add key value
-      add_key(fasta_seq[0..3].upcase)
+        #save all lengths
+        @sequence_lengths.push l
 
-      # add fasta length
-      @length_frequency[fasta_seq.length] = (@length_frequency[fasta_seq.length] || 1 ) + 1
+        # add key value
+        add_key(fasta_seq[0..3].upcase)
 
-      #extract qv values
-      extract_qv_from_sequence(qual) if @use_qual
+        # add fasta length
+        @length_frequency[fasta_seq.length] = (@length_frequency[fasta_seq.length] || 1 ) + 1
 
-      # print some progress info
-      if (sequence_reader.num_seqs % 10000==0)
-        puts "Calculating stats: #{sequence_reader.num_seqs}"
-      end
+        #extract qv values
+        extract_qv_from_sequence(qual) if @use_qual
 
+        # print some progress info
+        if (sequence_reader.num_seqs % 10000==0)
+          puts "Calculating stats: #{sequence_reader.num_seqs}"
+        end
+
+      end
     end
 
     length_stats = ScbiNArray.to_na(@sequence_lengths)
     length_frequency_stats = ScbiNArray.to_na(@length_frequency.map{|e| e || 0})
     quality_stats = ScbiNArray.to_na(@qv) if @use_qual
@@ -72,14 +75,14 @@
 
   def plot_lengths
 
     ## PLOT RESULTS
     if !File.exists?('graphs')
-    	Dir.mkdir('graphs')
+      Dir.mkdir('graphs')
     end
-    
 
+
     x = []
     y = []
 
     x =(0..@length_frequency.length-1).collect.to_a
     y = @length_frequency.map{|e| e || 0}
@@ -105,13 +108,13 @@
   end
 
   def plot_qualities
 
     if !File.exists?('graphs')
-    	Dir.mkdir('graphs')
+      Dir.mkdir('graphs')
     end
     minimum_qual_value = @params.get_param('min_quality').to_i
-    
+
     # get qualities values
     x=[]
     y=[]
     min=[]
     max=[]