plugin_linker.rb in seqtrimnext-2.0.41

- old
+ new

@@ -79,11 +79,11 @@
     end
   end
 
   def do_blasts(seqs)
      # find MIDS  with less results than max_target_seqs value 
-     blast = BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'linkers.fasta')}",'blastn'," -task blastn-short  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers          
+     blast = BatchBlast.new("-db #{@params.get_param('linkers_db')}",'blastn'," -task blastn-short  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers          
 
      $LOG.info('BLAST:'+blast.get_blast_cmd)
 
      fastas=[]
 
@@ -221,9 +221,13 @@
 		params.check_param(errors,'blast_evalue_linkers','Float',default_value,comment)
 		
 		comment='Minimum required identity (%) for a reliable linker'
 		default_value = 95
 		params.check_param(errors,'blast_percent_linkers','Integer',default_value,comment)
+
+    comment='Path for 454 linkers database'
+		default_value = File.join($FORMATTED_DB_PATH,'linkers.fasta')
+		params.check_param(errors,'linkers_db','DB',default_value,comment)
 		
     
     return errors
   end
   