plugin_user_contaminants.rb in seqtrimnext-2.0.66

- old
+ new

@@ -41,31 +41,45 @@
   def do_blasts(seqs)
 
     # TODO - Culling limit = 2 porque el blast falla con este comando cuando se le pasa cl=1 y dust=no
     # y una secuencia de baja complejidad como entrada
 
-    blast = BatchBlast.new("-db #{@params.get_param('user_contaminant_db')}",'blastn'," -task blastn -evalue #{@params.get_param('blast_evalue_user_contaminant')} -perc_identity #{@params.get_param('blast_percent_user_contaminant')} -culling_limit 1")  #get classify -max_target_seqs #{MAX_TARGETS_SEQS}
+    task_template=@params.get_param('blast_task_template_user_contaminants')
+    extra_params=@params.get_param('blast_extra_params_user_contaminants')
 
-    $LOG.debug('BLAST:'+blast.get_blast_cmd(:xml))
+    extra_params=extra_params.gsub(/^\"|\"?$/, '')
 
+    blast = BatchBlast.new("-db #{@params.get_param('user_contaminant_db')}",'blastn'," -task #{task_template} #{extra_params} -evalue #{@params.get_param('blast_evalue_user_contaminant')} -perc_identity #{@params.get_param('blast_percent_user_contaminant')} -culling_limit 1")  #get classify -max_target_seqs #{MAX_TARGETS_SEQS}
+
+    $LOG.debug('BLAST:'+blast.get_blast_cmd(:table))
+
     fastas=[]
 
     seqs.each do |seq|
       fastas.push ">"+seq.seq_name
       fastas.push seq.seq_fasta
     end
 
 
-    blast_table_results = blast.do_blast(fastas,:xml)
+    #blast_table_results = blast.do_blast(fastas,:xml)
+    t1=Time.now
+    blast_table_results = blast.do_blast(fastas,:table,false)
+    add_plugin_stats('execution_time','blast',Time.now-t1)
 
+    t1=Time.now
+    #blast_table_results = BlastStreamxmlResult.new(blast_table_results)
+    blast_table_results = BlastTableResult.new(blast_table_results)
+    add_plugin_stats('execution_time','parse',Time.now-t1)
+
+
     return blast_table_results
   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}"
+      raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
     end
 
     $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for classify into the sequence"
 
     type = "ActionUserContaminant"
@@ -141,9 +155,19 @@
     params.check_param(errors,'min_user_contaminant_size','Integer',default_value,comment)
 
     comment='Path for user contaminant database'
     default_value = "" #File.join($FORMATTED_DB_PATH,'user_contaminant.fasta')
     params.check_param(errors,'user_contaminant_db','DB',default_value,comment)
+
+    comment='Blast task template for user contaminations'
+    #default_value = 'blastn'
+    default_value = 'megablast'
+    params.check_param(errors,'blast_task_template_user_contaminants','String',default_value,comment)
+
+    comment='Blast extra params for user contaminations'
+    #default_value = ''
+    default_value = '"-word_size=22"'
+    params.check_param(errors,'blast_extra_params_user_contaminants','String',default_value,comment)
 
     return errors
   end
 
 