lib/seqtrimnext/plugins/plugin_amplicons.rb in seqtrimnext-2.0.51 vs lib/seqtrimnext/plugins/plugin_amplicons.rb in seqtrimnext-2.0.52

@@ -7,21 +7,9 @@
 # Inherit: Plugin
 ########################################################
 
 class PluginAmplicons < Plugin
 
-  # adapters found at end of sequence are even 2 nt wide, cut in 5 because of statistics
-  # MIN_PRIMER_SIZE = 5
-  # MIN_FAR_ADAPTER_SIZE = 13
-  # MIN_LEFT_ADAPTER_SIZE = 9
-  #Begins the plugin1's execution to warn that there are contaminants in the sequence "seq"
-  def execute(seqs)
-    blasts= do_blasts(seqs)
-
-    seqs.each_with_index do |s,i|
-      exec_seq(s,blasts.querys[i])
-    end
-  end
 
   def do_blasts(seqs)
     # find MIDS  with less results than max_target_seqs value
     blast=BatchBlast.new("-db #{@params.get_param('primers_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_primers')}")
     $LOG.debug('BLAST:'+blast.get_blast_cmd)