seqtrimnext 2.0.62 → 2.0.66

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1fb6845331e9b46e2a53f29312fce204869a91cf
-  data.tar.gz: 18d138fe1b899582daae2e4118cd6118853afc29
+  metadata.gz: ab74e9c551c43eb30da4a881ab544c9d7754ecaa
+  data.tar.gz: acdf2c4e6d4e5d36d5fafbe1e2004178ed33b145
 SHA512:
-  metadata.gz: d22ad436ce0b15ff783d15b871491adaa5947f9c1da4a7247712f7d6e9e790978ad90ab22657dc7768b51a61d6122f874c7853e9d0279f0dd408702a681ca5f0
-  data.tar.gz: 67d4af5e0bb8dc2eba127b6fe1ff04684c7b96db3fbad9e94cb6a222d88d4da3b5b5fd204022f70c0e14d2511ae476a7814f3ec32d21900c73f2370462207faa
+  metadata.gz: d60d9cb31be6eab17ff47e81e77ae3246408dee62f4061e040a9efdcfc9e6f54997e873e244a337091be391a00ca05eec2cd8d5da7b6ecdebf468b76540b5a39
+  data.tar.gz: bf2c6174ca48e5ea0d1bf9b7da3e58b01d89016674fa7050473a6dca2dc105d6156281c080e25d5906384a4587b7a51571b51ed9155043e0dee71546fff5ecb7

data/bin/resume_execution_times.rb

@@ -3,7 +3,7 @@
 require 'json'
 
 if ARGV.count<1 
-  puts "Usage: #{$0} [-t] [-j] stats1.json"
+  puts "Usage: #{$0} [-t] [-j] [-h] stats1.json"
   exit -1
 end
 
@@ -20,6 +20,15 @@ if ARGV[0]=='-j'
 	ARGV.shift
 end
 
+time_divider=1
+# print header  
+if ARGV[0]=='-h'
+	time_divider=3600
+	puts "Times are in hours"
+	ARGV.shift
+end
+
+
 
 ARGV.each do |file_path|
 	sample_name = File.basename(File.expand_path(File.join(file_path,'..','..')))
@@ -34,7 +43,7 @@ ARGV.each do |file_path|
 	begin
 		stats.keys.each do |k|
 			if stats[k]['execution_time']
-				res[k]=stats[k]['execution_time']['total_seconds']
+				res[k]=stats[k]['execution_time']['total_seconds'].to_f/time_divider
 				total+=res[k]
 			end
 		end
@@ -48,10 +57,10 @@ ARGV.each do |file_path|
 
 	if stats['scbi_mapreduce']
 		res['TOTAL_workers']=stats['scbi_mapreduce']['connected_workers']
-		res['TOTAL_read']=stats['scbi_mapreduce']['total_read_time']
-		res['TOTAL_write']=stats['scbi_mapreduce']['total_write_time']
-		res['TOTAL_manager_idle']=stats['scbi_mapreduce']['total_manager_idle_time']
-		res['TOTAL_execution']=stats['scbi_mapreduce']['total_seconds']
+		res['TOTAL_read']=stats['scbi_mapreduce']['total_read_time']/time_divider
+		res['TOTAL_write']=stats['scbi_mapreduce']['total_write_time']/time_divider
+		res['TOTAL_manager_idle']=stats['scbi_mapreduce']['total_manager_idle_time']/time_divider
+		res['TOTAL_execution']=stats['scbi_mapreduce']['total_seconds']/time_divider
 	end
 
 	if puts_json

data/bin/resume_stn_contaminants.rb

@@ -0,0 +1,37 @@
+#!/usr/bin/env ruby
+
+require 'json'
+
+if ARGV.count<1 
+  puts "Usage: #{$0} stats1.json [stats2.json stats3.json,...]"
+  exit -1
+end
+
+# print header  
+if ARGV[0]=='-t'
+	#heads=['sample_name','input_count','sequence_count_paired','sequence_count_single','rejected','rejected_percent']
+	#puts heads.join("\t")
+	ARGV.shift
+end
+
+contaminants={}
+
+ARGV.each do |file_path|
+	sample_name = File.basename(File.expand_path(File.join(file_path,'..','..')))
+
+	stats=JSON::parse(File.read(file_path))
+
+	res=[]
+	cont=stats['PluginContaminants']['contaminants_ids']
+
+	limit=60	
+	cont.keys.sort{|c1,c2| cont[c2].to_i <=> cont[c1].to_i}.each do |k|
+		#puts "#{k} => #{cont[k]}"
+		contaminants[k]=(contaminants[k] || 0 ) + cont[k]
+		limit = limit -1
+		break if limit==0
+	end
+
+end
+
+puts JSON::pretty_generate(contaminants)

data/bin/resume_stn_stats.rb

@@ -10,10 +10,11 @@ end
 # print header  
 if ARGV[0]=='-t'
 	heads=['sample_name','input_count','sequence_count_paired','sequence_count_single','rejected','rejected_percent']
-	puts heads.join("\t")   
+	puts heads.join("\t")
 	ARGV.shift
 end
 
+
 ARGV.each do |file_path|
 	sample_name = File.basename(File.expand_path(File.join(file_path,'..','..')))
 

data/bin/seqtrimnext

@@ -216,7 +216,7 @@ optparse = OptionParser.new do |opts|
         options[:workers] = Integer(workers)
       rescue
         STDERR.puts "ERROR:Invalid workers parameter #{options[:workers]}"
-        exit
+        exit -1
       end
 
     end
@@ -268,7 +268,7 @@ optparse = OptionParser.new do |opts|
     options[:format] = value
     if !['sanger','illumina15', 'illumina18'].include?(value)
       STDERR.puts "ERROR: Invalid FASTQ format parameter #{value}"
-      exit
+      exit -1
     end
   end
 
@@ -301,7 +301,7 @@ optparse = OptionParser.new do |opts|
     options[:template] = file
   end
 
-  options[:chunk_size] = 100
+  options[:chunk_size] = 5000
   opts.on( '-g', '--group_size chunk_size', 'Group sequences in chunks of size <chunk_size>' ) do |cs|
     options[:chunk_size] = cs.to_i
   end
@@ -332,7 +332,7 @@ optparse = OptionParser.new do |opts|
   opts.on_tail( '-h', '--help', 'Display this screen' ) do
     puts opts
     show_additional_help
-    exit
+    exit -1
   end
 end
 
@@ -342,13 +342,13 @@ optparse.parse!
 if options[:list_db] then
   # List database entries in a database
   ListDb.new($DB_PATH,options[:list_db_name])
-  exit
+  exit -1
 end
 
 if options[:gen_params] then
   # Generates a sample params file in current directory
   Params.generate_sample_params
-  exit
+  exit -1
 end
 
 #set logger
@@ -453,3 +453,5 @@ else
 
   $LOG.info "If you want a detailed report in PDF format, be sure you have installed the optional seqtrimnext_report gem (gem install seqtrimnext_report)#{skip_text}"
 end
+
+exit(Seqtrim.exit_status)

data/bin/split_fastq.rb

@@ -14,7 +14,7 @@ output_name = ARGV.shift
 split_by = ARGV.shift.to_i
 
 gz_arg=ARGV.shift
-gz=false
+gz=''
 
 if !gz_arg.nil? and gz_arg.index('-gz')
 	gz='.gz'

data/lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb

@@ -17,6 +17,7 @@ class SeqtrimWorkManager < ScbiMapreduce::WorkManager
     @@full_stats={}
     @@params= params
     @@exit = false
+    @@exit_status=0
 
     @@ongoing_stats={}
     @@ongoing_stats[:sequence_count] = 0
@@ -85,6 +86,10 @@ class SeqtrimWorkManager < ScbiMapreduce::WorkManager
 
   end
 
+  def self.exit_status
+    return @@exit_status
+  end
+
   def self.end_work_manager
 
     # if initial files doesn't exists, create it
@@ -115,6 +120,14 @@ class SeqtrimWorkManager < ScbiMapreduce::WorkManager
 
   end
 
+  def self.global_error_received(error_exception)
+    $LOG.error "Global error:\n" + error_exception.message + ":\n" +error_exception.backtrace.join("\n")
+    @@errors_file.puts "Global error:\n" + error_exception.message + ":\n" +error_exception.backtrace.join("\n")
+    @@errors_file.puts "="*60
+    @@exit_status=-1
+    SeqtrimWorkManager.controlled_exit
+  end
+
   def self.work_manager_finished
     @@full_stats['scbi_mapreduce']=@@stats
 
@@ -129,10 +142,14 @@ class SeqtrimWorkManager < ScbiMapreduce::WorkManager
   def error_received(worker_error, obj)
     @@errors_file.puts "Error while processing object #{obj.inspect}\n" + worker_error.original_exception.message + ":\n" +worker_error.original_exception.backtrace.join("\n")
     @@errors_file.puts "="*60
+    @@exit_status=-1
+    SeqtrimWorkManager.controlled_exit
+
   end
 
   def too_many_errors_received
     $LOG.error "Too many errors: #{@@error_count} errors on #{@@count} executed sequences, exiting before finishing"
+    @@exit_status=-1
   end
 
   def worker_initial_config

data/lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb

@@ -81,8 +81,8 @@ class SeqtrimWorker <  ScbiMapreduce::Worker
   def starting_worker
 
     # $WORKER_LOG.level = Logger::ERROR
-    $WORKER_LOG.level = Logger::WARN
-    #$WORKER_LOG.level = Logger::INFO
+    #$WORKER_LOG.level = Logger::WARN
+    $WORKER_LOG.level = Logger::INFO
     $WORKER_LOG.info "Loading actions"
 
     @action_manager = ActionManager.new

data/lib/seqtrimnext/classes/params.rb

@@ -33,8 +33,18 @@ class Params
         if !line.empty?
           if !(line =~ /^\s*#/)   # if line is not a comment
             # extract the parameter's name in params[0] and the parameter's value in params[1]
-            params = line.split(/\s*=\s*/)
+            #params = line.split(/\s*=\s*/)
 
+            # store in the hash the pair key/value, in our case will be name/numeric-value ,
+            # that are save in params[0] and params[1],  respectively
+            #if (!params[0].nil?) && (!params[1].nil?)
+            #  set_param(params[0].strip,params[1].strip,comments)
+            #  comments=[]
+            #end
+
+            line =~ /^\s*([^=]*)\s*=\s*(.*)\s*$/
+            params=[$1,$2]
+              
             # store in the hash the pair key/value, in our case will be name/numeric-value ,
             # that are save in params[0] and params[1],  respectively
             if (!params[0].nil?) && (!params[1].nil?)
@@ -42,7 +52,9 @@ class Params
               comments=[]
             end
 
-            #$LOG.debug "read: #{params[1]}"
+
+            $LOG.debug "read: #{params[0]}=#{params[1]}" if !$LOG.nil?
+            
           else
             comments << line.gsub(/^\s*#/,'')
           end # end if comentario

data/lib/seqtrimnext/classes/seqtrim.rb

@@ -15,6 +15,12 @@ require 'action_manager'
 
 class Seqtrim
   
+
+
+  def self.exit_status
+    return SeqtrimWorkManager.exit_status
+  end
+
   # First of all, reads the file's parameters, where are the values of all parameters and the 'plugin_list'  that specifies the order of execution from the plugins. 
   #
   # Secondly, loads the plugins in a folder .
@@ -24,7 +30,6 @@ class Seqtrim
   # After that, creates a thread's pool of a determinate number of workers, e.g. 10 threads,
   # reads the sequences from files 'fasta' , until now without qualities,
   # and executes the plugins over the sequences in the pool of threads
-  
 
   def get_custom_cdhit(cd_hit_input_file,params)
     cmd=''
@@ -136,7 +141,6 @@ class Seqtrim
 		default_value=Seqtrimnext::SEQTRIM_VERSION
 		params.check_param(errors,'seqtrim_version','String',default_value,comment)
 
-		
 		if !errors.empty?
           $LOG.error 'Please, define the following global parameters in params file:'
           errors.each do |error|
@@ -166,7 +170,7 @@ class Seqtrim
     if File.exists?(ScbiMapreduce::CHECKPOINT_FILE)
       if !options[:use_checkpoint]
         STDERR.puts "ERROR: A checkpoint file exists, either delete it or provide -C flag to use it"
-        exit
+        exit(-1)
       end
     end
     
@@ -230,7 +234,7 @@ class Seqtrim
 
     $LOG.info "Checking global params"
     if !check_global_params(params)
-    		exit
+    		exit(-1)
     end
                                    
     # Load actions
@@ -253,8 +257,7 @@ class Seqtrim
 
 	    	# save used params to file
         params.save_file('used_params.txt')
-
-      exit
+        exit(-1)
     end
     
     if !Dir.exists?(OUTPUT_PATH)
@@ -297,7 +300,7 @@ class Seqtrim
 	        params.load_repeated_seqs('clusters.fasta.clstr')
         else
           $LOG.error("Exiting due to not found clusters.fasta.clstr. Maybe cd-hit failed. Check cd-hit.out")
-          exit
+          exit(-1)
         end
 	    end
       
@@ -367,7 +370,12 @@ class Seqtrim
 				sequence_readers.each do |file|
 				  file.close
 				end
-				
+
+        if SeqtrimWorkManager.exit_status>=0
+				  $LOG.info "Exit status: #{SeqtrimWorkManager.exit_status}"
+        else
+          $LOG.error "Exit status: #{SeqtrimWorkManager.exit_status}"
+        end
 				$LOG.info 'Closing server'
 			end
 			

data/lib/seqtrimnext/plugins/plugin.rb

@@ -23,12 +23,15 @@ class Plugin
       t1=Time.now
       execute(seq)
       t2=Time.now
+
+      add_plugin_stats('execution_time','total_seconds',t2-t1)
     end
     
-    
-    @stats['execution_time']={}
+  end
 
-    @stats['execution_time']['total_seconds']=t2-t1
+  def add_plugin_stats(cat,item,elapsed_time)
+      @stats[cat]={} if @stats[cat].nil?
+      @stats[cat][item]=elapsed_time
   end
 
   def can_execute?
@@ -40,7 +43,9 @@ class Plugin
 
   #Begins the plugin's execution whit the sequence "seq"
   def execute(seqs)
+    t1=Time.now
     blasts=do_blasts(seqs)
+    
 
     if !blasts.empty?
       
@@ -49,18 +54,24 @@ class Plugin
       else
         queries = blasts.querys
       end
-      
+
+      add_plugin_stats('execution_time','blast_and_parse',Time.now-t1)
+
+      t1=Time.now
       seqs.each_with_index do |s,i|
         exec_seq(s,queries[i])
       end
 
     else # there is no blast
 
+      t1=Time.now
       seqs.each do |s|
         exec_seq(s,nil)
       end
-
     end
+
+    add_plugin_stats('execution_time','exec_seq',Time.now-t1)
+
   end
 
   def do_blasts(seqs)

data/lib/seqtrimnext/plugins/plugin_ab_adapters.rb

@@ -18,6 +18,9 @@ class PluginAbAdapters < Plugin
     
     # find MIDS  with less results than max_target_seqs value 
     blast=BatchBlast.new("-db #{@params.get_param('adapters_ab_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_ab')} -word_size #{MIN_ADAPTER_SIZE}")  
+
+    # con culling limit hay situaciones en las que un hit largo con 1 mismatch es ignorado porque hay otro más corto que no tiene ningun error, no es aceptable.
+    #blast=BatchBlast.new("-db #{@params.get_param('adapters_ab_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_ab')} -word_size #{MIN_ADAPTER_SIZE} -culling_limit=1")  
     $LOG.debug('BLAST:'+blast.get_blast_cmd)
 
     fastas=[]
@@ -29,7 +32,32 @@ class PluginAbAdapters < Plugin
     
     # fastas=fastas.join("\n")
     
-    blast_table_results = blast.do_blast(fastas)
+    #blast_table_results = blast.do_blast(fastas)
+    #blast_table_results = BlastTableResult.new(blast_table_results)
+
+    
+    t1=Time.now
+    blast_table_results = blast.do_blast(fastas,:table,false)
+    add_plugin_stats('execution_time','blast',Time.now-t1)
+
+    
+    #f=File.new("/tmp/salida_#{fastas.first.gsub('>','').gsub('/','_')}.blast",'w+')
+    #f.puts blast.get_blast_cmd
+    #f.puts blast_table_results
+    #f.close
+
+    t1=Time.now
+    blast_table_results = BlastTableResult.new(blast_table_results)
+    add_plugin_stats('execution_time','parse',Time.now-t1)
+
+
+    # t1=Time.now
+    # blast_table_results = blast.do_blast(fastas,:xml,false)
+    # add_plugin_stats('execution_time','blast',Time.now-t1)
+
+    # t1=Time.now
+    # blast_table_results = BlastStreamxmlResult.new(blast_table_results)
+    # add_plugin_stats('execution_time','parse',Time.now-t1)
     
     # puts blast_table_results.inspect
    

data/lib/seqtrimnext/plugins/plugin_adapters.rb

@@ -27,7 +27,7 @@ class PluginAdapters < Plugin
     
     # fastas=fastas.join("\n")
     
-    blast_table_results = blast.do_blast(fastas,:xml)
+    blast_table_results = blast.do_blast(fastas,:table)
     
     # puts blast_table_results.inspect
    

data/lib/seqtrimnext/plugins/plugin_contaminants.rb

@@ -23,12 +23,22 @@ class PluginContaminants < Plugin
     # find MIDS  with less results than max_target_seqs value
     # blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}
 
+    # This message is due to short sequences
+    #Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options 
+
     # 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('contaminants_db')}",'blastn'," -task blastn -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}
+    task_template=@params.get_param('blast_task_template_contaminants')
+    extra_params=@params.get_param('blast_extra_params_contaminants')
+
+    extra_params=extra_params.gsub(/^\"|\"?$/, '')
+
+    #blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task blastn  -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}
+
+    blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task #{task_template} #{extra_params} -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}
 
-    $LOG.debug('BLAST:'+blast.get_blast_cmd(:xml))
+    $LOG.debug('BLAST:'+blast.get_blast_cmd(:table))
 
     fastas=[]
 
@@ -43,7 +53,16 @@ class PluginContaminants < Plugin
     # $LOG.info(fastas)
     # $LOG.info('-'*20)
 
-    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,:xml,false)
+    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)
 
     # $LOG.info(blast_table_results.inspect)
 
@@ -62,12 +81,14 @@ class PluginContaminants < Plugin
       return
     end
     
+    #if blast_query.query_def != seq.seq_name
     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 contaminants into the sequence"
 
+    #add_plugin_stats('hsp_count',seq.seq_name,blast_query.hits.count) 
 
     #blast = BatchBlast.new('-db DB/formatted/contaminants.fasta','blastn',' -task blastn -evalue 1e-10 -perc_identity 95')  #get contaminants
     # blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}
@@ -195,11 +216,19 @@ class PluginContaminants < Plugin
     default_value = 'true'
     params.check_param(errors,'contaminants_reject','String',default_value,comment)
 
-
     comment='Path for contaminants database'
     default_value = File.join($FORMATTED_DB_PATH,'contaminants.fasta')
     params.check_param(errors,'contaminants_db','DB',default_value,comment)
 
+    comment='Blast task template for contaminations'
+    #default_value = 'blastn'
+    default_value = 'megablast'
+    params.check_param(errors,'blast_task_template_contaminants','String',default_value,comment)
+
+    comment='Blast extra params for contaminations'
+    #default_value = ''
+    default_value = '"-word_size=22"'
+    params.check_param(errors,'blast_extra_params_contaminants','String',default_value,comment)
 
     return errors
   end

data/lib/seqtrimnext/plugins/plugin_low_complexity.rb

@@ -73,6 +73,7 @@ class PluginLowComplexity < Plugin
       
       if !actions.empty?
         add_stats('low_complexity',total_dust)
+        seq.add_file_tag(0, 'low_complexity', :both, 100)
         seq.add_actions(actions)
       end
 
@@ -92,6 +93,7 @@ class PluginLowComplexity < Plugin
     # default_value = 80
     # params.check_param(errors,'poly_t_percent','Integer',default_value,comment)
     # 
+
     return errors
   end
 

data/lib/seqtrimnext/plugins/plugin_low_quality.rb

@@ -170,9 +170,10 @@ class PluginLowQuality < Plugin
 		default_value = 20
 		params.check_param(errors,'min_quality','Integer',default_value,comment)
 		
-	  comment='Quality window for scanning low quality segments'
-		default_value = 15
-		params.check_param(errors,'window_width','Integer',default_value,comment)
+    
+	  #comment='Quality window for scanning low quality segments'
+		#default_value = 15
+		#params.check_param(errors,'window_width','Integer',default_value,comment)
    
     
 	  comment='Minimum length of a bad quality segment inside the sequence'

data/lib/seqtrimnext/plugins/plugin_user_contaminants.rb

@@ -43,9 +43,14 @@ class PluginUserContaminants < Plugin
     # 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=[]
 
@@ -55,7 +60,16 @@ class PluginUserContaminants < Plugin
     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
@@ -63,7 +77,7 @@ class PluginUserContaminants < Plugin
 
   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
 
     $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for classify into the sequence"
@@ -144,6 +158,16 @@ class PluginUserContaminants < Plugin
     default_value = "" #File.join($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
 

data/lib/seqtrimnext/plugins/plugin_vectors.rb

@@ -40,7 +40,17 @@ class PluginVectors < Plugin
 
     # fastas=fastas.join("\n")
 
-    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)
+
 
     # puts blast_table_results.inspect
 
@@ -50,7 +60,7 @@ class PluginVectors < Plugin
 
  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 vectors into the sequence " 

data/lib/seqtrimnext/version.rb

@@ -1,4 +1,4 @@
 module Seqtrimnext
-  VERSION = "2.0.62"
+  VERSION = "2.0.66"
   SEQTRIM_VERSION = VERSION
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: seqtrimnext
 version: !ruby/object:Gem::Version
-  version: 2.0.62
+  version: 2.0.66
 platform: ruby
 authors:
 - Dario Guerrero
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-01-20 00:00:00.000000000 Z
+date: 2016-05-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -219,6 +219,7 @@ executables:
 - resume_clusters.rb
 - resume_execution_times.rb
 - resume_rejected.rb
+- resume_stn_contaminants.rb
 - resume_stn_stats.rb
 - reverse_paired.rb
 - seqtrimnext
@@ -252,6 +253,7 @@ files:
 - bin/resume_clusters.rb
 - bin/resume_execution_times.rb
 - bin/resume_rejected.rb
+- bin/resume_stn_contaminants.rb
 - bin/resume_stn_stats.rb
 - bin/reverse_paired.rb
 - bin/seqtrimnext
@@ -380,7 +382,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.4
+rubygems_version: 2.4.8
 signing_key: 
 specification_version: 4
 summary: Sequences preprocessing and cleaning software