plugin_ab_adapters.rb in seqtrimnext-2.0.35

- old
+ new

@@ -41,10 +41,22 @@
     # puts blast_table_results.inspect
    
     return blast_table_results
  end
  
+ # filter hits that are far the extreme and do not have a valid length
+ def filter_hits(hits,end_pos)
+   hits.reverse_each do |hit|
+    if (hit.q_end < (end_pos-40)) && ((hit.q_end-hit.q_beg+1)<(@params.get_ab_adapter(hit.subject_id).length*0.80).to_i)
+      hits.delete(hit)
+    #   puts "DELETE #{hit.inspect}"
+    # else
+    #   puts "ACCEPTED #{hit.inspect}, >= #{(@params.get_ab_adapter(hit.subject_id).length*0.2).to_i}"
+    end
+   end
+   
+ end
  
  def exec_seq(seq,blast_query)
    if blast_query.query_id != seq.seq_name
      raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
    end
@@ -60,12 +72,14 @@
     #---------------------------------------------------------------------
     
     # blast_table_results = blast.do_blast(seq.seq_fasta)             #rise seq to adapterss  executing over blast
     
      #BlastTableResult.new(res)
-     # puts blast.get_blast_cmd
+     # puts blast_query.inspect
      # puts blast_table_results.inspect
+     
+     filter_hits(blast_query.hits, seq.seq_fasta.length)
     
     adapters=[]
     # blast_table_results.querys.each do |query|     # first round to save adapters without overlap
       merge_hits(blast_query.hits,adapters)
     # end
@@ -74,9 +88,13 @@
       adapters2=adapters                            # second round to save adapters without overlap
       adapters = []
       merge_hits(adapters2,adapters)
     end until (adapters2.count == adapters.count)
 
+    # puts "MERGED"
+    # puts "="*50
+    # adapters.each {|a| puts a.inspect}
+    
     max_to_end=@params.get_param('max_ab_to_end').to_i
     # type = 'ActionAbAdapter'
     actions=[]   
     adapter_size=0 
     