plugin_ignore_repeated.rb in seqtrimnext-2.0.52

- old
+ new

@@ -11,17 +11,11 @@
 class PluginIgnoreRepeated < Plugin
 
  SIZE_SEARCH_IN_IGNORE=15
  
  #Begins the plugin1's execution to warn that there are repeated sequences,  and disables all but one"
-def execute(seqs)
-   seqs.each do |s|
-     exec_seq(s)
-   end
- end
+ def exec_seq(seq,blast_query)
 
-
- def exec_seq(seq)
     $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: searching sequence repeated at input file" 
 
     fasta_input=@params.get_param('truncated_input_file')
     
     blast = BatchBlast.new("-db #{fasta_input}" ,'blastn'," -task blastn-short -searchsp #{SIZE_SEARCH_IN_IGNORE} -evalue #{@params.get_param('blast_evalue_ignore_repeated')} -perc_identity #{@params.get_param('blast_percent_ignore_repeated')}")  #get contaminants