plugin_low_complexity.rb in seqtrimnext-2.0.52

- old
+ new

@@ -10,23 +10,14 @@
 require "plugin"
 
 MIN_DUST_SIZE = 30
 
 class PluginLowComplexity < Plugin
-
-
-
-  def execute(seqs)
-    dust= do_dust(seqs)
-    
-    seqs.each_with_index do |s,i|
-      exec_seq(s,dust[i])
-    end
-  end
   
-  def do_dust(seqs)
-     # find MIDS  with less results than max_target_seqs value 
+  # do the dust masker instead of blast
+  def do_blasts(seqs)
+
      dust_masker=DustMasker.new()
 
      fastas=[]
      
      seqs.each do |seq|
@@ -42,11 +33,13 @@
     
      return found_dust
   end
   
   
-  def exec_seq(seq,dust_query)
+  def exec_seq(seq,blast_query)
+    dust_query=blast_query
+    
     if dust_query.query_id != seq.seq_name
       raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
     end
     actions=[]
 
@@ -63,17 +56,9 @@
           
 
           if (dust_size)>=MIN_DUST_SIZE
           
             # check if low complexity is inside a lowqual region
-            # in_low_qual=false
-            # low_quals.each do |lq|
-            #   if lq.contains_action?(start,stop,0)
-            #     in_low_qual=true
-            #     break
-            #   end
-            # end
-            
             if !seq.range_inside_action_type?(start,stop,ActionLowQuality)
               
               total_dust+=dust_size    
               a = seq.new_action(start,stop,'ActionLowComplexity')
               # a.left_action=true