seqtrimnext 2.0.51 → 2.0.52

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

@@ -2,25 +2,25 @@
 #finds the classes that were in the folder 'classes'
 
 # ROOT_PATH=File.dirname(File.dirname(File.dirname(__FILE__)))
-# 
+#
 # $: << File.expand_path(File.join(ROOT_PATH, 'classes'))
 # $: << File.expand_path(File.join(ROOT_PATH, 'classes','blast'))
-# 
+#
 # #finds the classes that were in the folder 'plugins'
 # $: << File.expand_path(File.join(ROOT_PATH, 'plugins'))
-# 
+#
 # #finds the classes that were in the folder 'plugins'
 # $: << File.expand_path(File.join(ROOT_PATH, 'actions'))
-# 
+#
 # #finds the classes that were in the folder 'utils'
 # $: << File.expand_path(File.join(ROOT_PATH, 'utils'))
-# 
+#
 # $: << File.expand_path(File.join(ROOT_PATH, 'classes','em_classes'))
-# 
+#
 # $: << File.expand_path(ROOT_PATH)
 
 $: << File.expand_path('~/progs/ruby/gems/seqtrimnext/lib/')
-$: << File.expand_path('~/progs/ruby/gems/scbi_mapreduce/lib')
+# $: << File.expand_path('~/progs/ruby/gems/scbi_mapreduce/lib')
 
 require 'seqtrimnext'
 
@@ -32,7 +32,7 @@ if ENV['BLASTDB']# && Dir.exists?(ENV['BLASTDB'])
   $DB_PATH = File.dirname($FORMATTED_DB_PATH)
 else
   $FORMATTED_DB_PATH = File.expand_path(File.join(ROOT_PATH, "DB",'formatted'))
-  $DB_PATH = File.expand_path(File.join(ROOT_PATH, "DB"))  
+  $DB_PATH = File.expand_path(File.join(ROOT_PATH, "DB"))
 end
 
 ENV['BLASTDB']=$FORMATTED_DB_PATH
@@ -47,254 +47,389 @@ require 'params'
 require 'action_manager'
 require 'plugin_manager'
 # require 'sequence_with_action'
-# 
+#
 require 'scbi_fastq'
 require 'sequence_group'
 
 class SeqtrimWorker <  ScbiMapreduce::Worker
 
-    def process_object(obj)
-          running_seqs=SequenceGroup.new(obj)
-          
-         # execute plugins
-         @plugin_manager.execute_plugins(running_seqs)
-         
-         # add output data
-          add_output_data(running_seqs)
-         
-			   return running_seqs
-		end
-		
-    def receive_initial_config(obj)
-
-				# Reads the parameters
-				$WORKER_LOG.info "Params received"
-#				@params = Params.new(params_path)
-				@params = obj
-				
-				@use_qual=@params.get_param('use_qual')
-				@use_json=@params.get_param('use_json')
-    end
+  def process_object(obj)
 
-		def starting_worker
-
-        # $WORKER_LOG.level = Logger::ERROR
-        $WORKER_LOG.level = Logger::WARN
-				$WORKER_LOG.info "Loading actions"
-
-				@action_manager = ActionManager.new
-
-				$WORKER_LOG.info "Loading plugins"
-				@plugin_list = @params.get_param('plugin_list') # puts in plugin_list the plugins's array
-				$WORKER_LOG.info "PLUGIN LIST:" + @plugin_list
-				
-				@plugin_manager = PluginManager.new(@plugin_list,@params) # creates an instance from PluginManager. This must storage the plugins and load it    
-		
-		rescue Exception => e
-			puts (e.message+ e.backtrace.join("\n"))
-		
-		end
-		
-		
-		def closing_worker
-			 
-		end		
-		
-		
-		def add_output_data(obj)
-      obj.output_text=[]
-      
-		  obj.each do |seq|
-		    	obj.output_text << seq.to_text
-          write_seq_to_files(obj.output_files,seq, obj.stats)
-		  end
-		  
-      # @remove seqs since they are not needed anymore to write output files
-      obj.remove_all_seqs
-	  end
-	  
-	  def add_stat(stats,key,subkey,value,count=1)
-	    
-	    stats[key]={} if !stats[key]
-      stats[key][subkey]={} if !stats[key][subkey]
-      stats[key][subkey][value]=0 if !stats[key][subkey][value]
-      
-  	  stats[key][subkey][value]+=count
-    end
+    running_seqs=SequenceGroup.new(obj.flatten)
 
-  	def write_seq_to_files(files,seq, stats)
-      # puts stats.to_json
-      
-      dir_name,file_name=seq.get_file_tag_path
-      # puts File.join(dir_name,'sequences_'+file_name)
-      
-      # get current inserts
-      inserts = seq.get_inserts
-      
-      # qualities are optional
-      if @use_qual
-        qual_inserts = seq.get_qual_inserts
- 	    end
-      
-      # save json if necessary
-      if @use_json
-        json_file(files)<< seq.to_json
-      end
-      
-      # find mids
-      mid = seq.get_actions(ActionMid).first
-      
-      
-      if (seq.seq_rejected)           # sequence rejected
-      
-      	#save to rejected sequences 
-        message = seq.seq_rejected_by_message 
-        rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + message)
-        
-        add_stat(stats,'sequences','rejected',seq.seq_rejected_by_message)
-        add_stat(stats,'sequences','count','rejected')
-    	  
-
-      elsif (inserts.empty?)  #sequence with no inserts
-        message = 'No valid inserts found'
-        rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + message)
-        
-        add_stat(stats,'sequences','rejected',message)
-        add_stat(stats,'sequences','count','rejected')
-        
-			elsif (inserts.count == 2) # sequence with two inserts  = PAIRED SEQUENCES
-        add_stat(stats,'sequences','count','output_seqs_paired')
-
-        # TODO - Add this stats to full stats
-        # @@full_stats.add_stats({'sequences' => {'paired' => {'count' => 1}}})
-  	    
-				if (mid.nil? || (mid.message=='no_MID') ) # without mid
-					mid_id = 'no_MID'
-					mid_message = ' No MID found'
-				else
-					mid_id = mid.tag_id
-					mid_message=''
-					if mid_id != mid_message
-						mid_message = ' '+mid.message
-					end
-				end
-
-        # fasta_file = get_paired_file(mid_id)
-
-        n="#{seq.seq_name}_left"
-        c="template=#{seq.seq_name} dir=R library=#{mid_id}"
-        f=inserts[0].reverse.tr('actgACTG','tgacTGAC')
-        q=[]
-        if @use_qual
-            q=qual_inserts[0].reverse			    
-   	    end   
-
-        paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
-        
-        
-        n="#{seq.seq_name}_right"
-        c="template=#{seq.seq_name} dir=F library=#{mid_id}"
-        f=inserts[1]
-        q=[]
-        if @use_qual
-	          q=qual_inserts[1]
-   	    end
-        
-        paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
-        
-        
-      elsif (inserts.count == 1) # sequence with one insert
-
-				if (mid.nil? || (mid.message=='no_MID') ) # without mid
-					mid_id = 'no_MID'
-					mid_message = ' No MID found'
-				else
-					mid_id = mid.tag_id
-					mid_message=''
-					if mid_id != mid_message
-						mid_message = ' '+mid.message
-					end
-				end
-
-       # save fasta and qual in no MID file
-        has_low_complexity = seq.get_actions(ActionLowComplexity)
-        
-        if has_low_complexity.empty?
-          add_stat(stats,'sequences','count','output_seqs')
-          
-          # fasta_file = get_sequence_file(mid_id)
-          # sff_file=get_sffinfo_file(mid_id)
-          fasta_file=sequence_file(files,dir_name,file_name)
-          sff_file=sffinfo_file(files,dir_name,file_name)
-        else
-          add_stat(stats,'sequences','count','output_seqs_low_complexity')
-          
-          # fasta_file = get_low_complexity_file(mid_id)
-          # sff_file=get_low_sffinfo_file(mid_id)
-          fasta_file=low_complexity_file(files,dir_name,file_name)
-          sff_file=low_sffinfo_file(files,dir_name,file_name)
+    # execute plugins
+    @plugin_manager.execute_plugins(running_seqs)
+
+    # add output data
+    add_output_data(running_seqs)
+
+    return running_seqs
+  end
+
+  def receive_initial_config(obj)
+
+    # Reads the parameters
+    $WORKER_LOG.info "Params received"
+    #				@params = Params.new(params_path)
+    @params = obj
+    @tuple_size=@params.get_param('tuple_size')
+
+    @use_qual=@params.get_param('use_qual')
+    @use_json=@params.get_param('use_json')
+  end
+
+  def starting_worker
+
+    # $WORKER_LOG.level = Logger::ERROR
+    $WORKER_LOG.level = Logger::WARN
+    $WORKER_LOG.info "Loading actions"
+
+    @action_manager = ActionManager.new
+
+    $WORKER_LOG.info "Loading plugins"
+    @plugin_list = @params.get_param('plugin_list') # puts in plugin_list the plugins's array
+    $WORKER_LOG.info "PLUGIN LIST:" + @plugin_list
+
+    @plugin_manager = PluginManager.new(@plugin_list,@params) # creates an instance from PluginManager. This must storage the plugins and load it
+
+  rescue Exception => e
+    puts (e.message+ e.backtrace.join("\n"))
+
+  end
+
+
+  def closing_worker
+
+  end
+
+
+  def add_output_data(obj)
+    obj.output_text=[]
+
+    if @tuple_size>1
+      obj.each_slice(@tuple_size) do |seqs|
+
+        write_seq_to_files_tuple(obj.output_files,seqs, obj.stats)
+
+        seqs.each do |seq|
+          obj.output_text << seq.to_text
         end
-        
-        q=[]
-        if @use_qual
-	         q=qual_inserts[0]
-				end
-        
-        n=seq.seq_name
-        c=mid_message
-        f=inserts[0]
-        
-        fasta_file << FastqFile.to_fastq(n,f,q,c)
-        
-        inserts_pos = seq.get_actions(ActionInsert)
-        
-        sff_file<< "#{n} #{inserts_pos[0].start_pos+1} #{inserts_pos[0].end_pos+1}"
-        
       end
-  	  
-	  end
-	  
-	  
-	  # ACCESS TO FILES
-
-	  def json_file(files)
-      return get_file(files,File.join(OUTPUT_PATH,'results.json'))
-	  end
-	  
-	  def rejected_output_file(files)
-      return get_file(files,File.join(OUTPUT_PATH,'rejected.txt'))
-	  end
-	  
-	  
-	  def sequence_file(files, dir_name, file_name)
-      return get_file(files,File.join(OUTPUT_PATH,dir_name,'sequences_'+file_name+'.fastq'))
-	  end 	
-	  
-    def paired_file(files, dir_name, file_name)
-      return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_'+file_name+'.fastq'))
+
+    else
+      obj.each do |seq|
+        write_seq_to_files_normal(obj.output_files,seq, obj.stats)
+        obj.output_text << seq.to_text
+      end
+    end
+
+    # @remove seqs since they are not needed anymore to write output files
+    obj.remove_all_seqs
+  end
+
+  def add_stat(stats,key,subkey,value,count=1)
+
+    stats[key]={} if !stats[key]
+    stats[key][subkey]={} if !stats[key][subkey]
+    stats[key][subkey][value]=0 if !stats[key][subkey][value]
+
+    stats[key][subkey][value]+=count
+  end
+
+  def write_seq_to_files_tuple(files,seqs, stats)
+
+    
+    seq1=seqs[0]
+    seq2=seqs[1]
+    
+    dir_name,file_name,priority=seq1.get_file_tag_path
+    dir_name2,file_name2,priority2=seq2.get_file_tag_path
+    
+    # both paired sequences must go in same file, there are priorities
+    if (dir_name!=dir_name2) || (file_name!=file_name2)
+      if priority2>priority
+        dir_name=dir_name2
+        file_name=file_name2
+      end
     end
+    
+    # get current inserts
+    inserts1 = seq1.get_inserts
+    inserts2 = seq2.get_inserts
 
-    def low_complexity_file(files, dir_name, file_name)
-      return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_'+file_name+'.fastq'))
+    # qualities are optional
+    if @use_qual
+      qual_inserts1 = seq1.get_qual_inserts
+      qual_inserts2 = seq2.get_qual_inserts
     end
-	  
-	  def sffinfo_file(files, dir_name, file_name)
-      return get_file(files,File.join(OUTPUT_PATH,dir_name,'sff_info_'+file_name+'.txt'))
+    
+    
+    
+    # save json if necessary
+    if @use_json
+      json_file(files)<< seq1.to_json
+      json_file(files)<< seq2.to_json
     end
 
-	  def low_sffinfo_file(files, dir_name, file_name)
-      return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_sff_info_'+file_name+'.txt'))
+    # find mids
+    mid1 = seq1.get_actions(ActionMid).first
+    mid2 = seq2.get_actions(ActionMid).first
+    
+    
+    if !inserts1.empty? && !inserts2.empty? # both have inserts
+      # save_two_inserts(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name)
+      save_two_inserts_tuple(files,seq1,seq2, stats,inserts1,inserts2,qual_inserts1,qual_inserts2,mid1,dir_name,file_name)
+    else
+      save_rejected_empty_or_single(files,seq1, stats,inserts1,qual_inserts1,mid1,dir_name,file_name)
+      save_rejected_empty_or_single(files,seq2, stats,inserts2,qual_inserts2,mid2,dir_name,file_name)
+    end
+    
+  end
+  
+  def save_two_inserts_tuple(files,seq1,seq2, stats,inserts1,inserts2,qual_inserts1,qual_inserts2,mid,dir_name,file_name)
+    
+    add_stat(stats,'sequences','count','output_seqs_paired')
+    add_stat(stats,'sequences','count','output_seqs_paired')
+
+    mid_id,mid_message=get_mid_message(mid)
+
+    # save left read
+    n="#{seq1.seq_name}"
+    c=seq1.get_comment_line # "template=#{seq1.seq_name} dir=R library=#{mid_id}"
+    f=inserts1[0]#.reverse.tr('actgACTG','tgacTGAC')
+    q=[]
+    if @use_qual
+      q=qual_inserts1[0] #.reverse
     end
-	  
-	  def get_file(files,fn)
-	    res=files[fn]
-	    
-	    if !res
-	      files[fn]=[]
-	      res=files[fn]
+    
+    paired_file_ilu1(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
+    
+    # save right read
+    n="#{seq2.seq_name}"
+    c=seq2.get_comment_line # "template=#{seq2.seq_name} dir=F library=#{mid_id}"
+    f=inserts2[0]
+    q=[]
+    if @use_qual
+      q=qual_inserts2[0]
+    end
+
+    paired_file_ilu2(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
+    
+  end
+  
+  
+  def save_rejected_empty_or_single(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name)
+    if (seq.seq_rejected) # save to rejected sequences
+      save_rejected_seq(files,seq, stats)
+    elsif (inserts.empty?)  #sequence with no inserts
+      save_empty_insert(files,seq, stats)
+    elsif (inserts.count == 1) # sequence with one insert
+      save_one_insert(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name)
+    end
+  end
+  
+  
+  #  SAVE NORMAL ===============================
+  def save_rejected_seq(files,seq, stats)
+    # message = seq.seq_rejected_by_message
+    message= seq.get_comment_line
+    rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + message)
+
+    add_stat(stats,'sequences','rejected',seq.seq_rejected_by_message)
+    add_stat(stats,'sequences','count','rejected')
+  end
+  
+  def save_empty_insert(files,seq, stats)
+    seq.seq_rejected=true
+    seq.seq_rejected_by_message='short insert'
+
+    message = 'No valid inserts found'
+
+    rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + message)
+
+    add_stat(stats,'sequences','rejected',message)
+    add_stat(stats,'sequences','count','rejected')
+    
+  end
+  
+  def get_mid_message(mid)
+    if (mid.nil? || (mid.message=='no_MID') ) # without mid
+      mid_id = 'no_MID'
+      mid_message = ' No MID found'
+    else
+      mid_id = mid.tag_id
+      mid_message=''
+      if mid_id != mid_message
+        mid_message = ' '+mid.message
       end
+    end
+    return mid_id,mid_message
+  end
+  
+  def save_two_inserts(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name)
+    add_stat(stats,'sequences','count','output_seqs_paired')
+
+    mid_id,mid_message=get_mid_message(mid)
+
+    # save left read
+    n="#{seq.seq_name}_left"
+    c="template=#{seq.seq_name} dir=R library=#{mid_id} #{seq.get_comment_line}"
+    f=inserts[0].reverse.tr('actgACTG','tgacTGAC')
+    q=[]
+    if @use_qual
+      q=qual_inserts[0].reverse
+    end
+    
+    paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
+    
+    # save right read
+    n="#{seq.seq_name}_right"
+    c="template=#{seq.seq_name} dir=F library=#{mid_id}  #{seq.get_comment_line}"
+    f=inserts[1]
+    q=[]
+    if @use_qual
+      q=qual_inserts[1]
+    end
+
+    paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c)
+    
+  end
+  
+  def save_one_insert(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name)
+    mid_id,mid_message=get_mid_message(mid)
+
+    # save fasta and qual in no MID file
+    has_low_complexity = seq.get_actions(ActionLowComplexity)
+
+    if has_low_complexity.empty?
+      add_stat(stats,'sequences','count','output_seqs')
+
+      fasta_file=sequence_file(files,dir_name,file_name)
+      sff_file=sffinfo_file(files,dir_name,file_name)
+    else
+      add_stat(stats,'sequences','count','output_seqs_low_complexity')
+
+      fasta_file=low_complexity_file(files,dir_name,file_name)
+      sff_file=low_sffinfo_file(files,dir_name,file_name)
+    end
+
+    q=[]
+    if @use_qual
+      q=qual_inserts[0]
+    end
+
+    n=seq.seq_name
+    c=mid_message
+
+    seq_comments=seq.get_comment_line
+    if !seq_comments.strip.empty?
+      c=seq_comments + c
+    end
+
+    f=inserts[0]
+
+    fasta_file << FastqFile.to_fastq(n,f,q,c)
+
+    inserts_pos = seq.get_actions(ActionInsert)
+
+    sff_file<< "#{n} #{inserts_pos[0].start_pos+1} #{inserts_pos[0].end_pos+1}"
+    
+    
+  end
+
+
+  def write_seq_to_files_normal(files,seq, stats)
+
+    # puts stats.to_json
+
+    dir_name,file_name,priority=seq.get_file_tag_path
+    # puts File.join(dir_name,'sequences_'+file_name)
+
+    # get current inserts
+    inserts = seq.get_inserts
+
+    # qualities are optional
+    if @use_qual
+      qual_inserts = seq.get_qual_inserts
+    end
+
+    # save json if necessary
+    if @use_json
+      json_file(files)<< seq.to_json
+    end
+
+    # find mids
+    mid = seq.get_actions(ActionMid).first
+
+
+    if (seq.seq_rejected) # save to rejected sequences
+      save_rejected_seq(files,seq, stats)
       
-      return res
+    elsif (inserts.empty?)  #sequence with no inserts
+      save_empty_insert(files,seq, stats)
+      
+    elsif (inserts.count == 2) # sequence with two inserts  = PAIRED SEQUENCES
+      save_two_inserts(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name)
+      
+    elsif (inserts.count == 1) # sequence with one insert
+      save_one_insert(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name)
+    end
+
+  end
+  
+  
+  
+
+
+  # ACCESS TO FILES
+
+  def json_file(files)
+    return get_file(files,File.join(OUTPUT_PATH,'results.json'))
+  end
+
+  def rejected_output_file(files)
+    return get_file(files,File.join(OUTPUT_PATH,'rejected.txt'))
+  end
+
+
+  def sequence_file(files, dir_name, file_name)
+    return get_file(files,File.join(OUTPUT_PATH,dir_name,'sequences_'+file_name+'.fastq'))
+  end
+
+  def paired_file(files, dir_name, file_name)
+    return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_'+file_name+'.fastq'))
+  end
+  
+  def paired_file_ilu1(files, dir_name, file_name)
+    return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_1_'+file_name+'.fastq'))
+  end
+
+  def paired_file_ilu2(files, dir_name, file_name)
+    return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_2_'+file_name+'.fastq'))
+  end
+  
+
+  def low_complexity_file(files, dir_name, file_name)
+    return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_'+file_name+'.fastq'))
+  end
+
+  def sffinfo_file(files, dir_name, file_name)
+    return get_file(files,File.join(OUTPUT_PATH,dir_name,'sff_info_'+file_name+'.txt'))
+  end
+
+  def low_sffinfo_file(files, dir_name, file_name)
+    return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_sff_info_'+file_name+'.txt'))
+  end
+
+  def get_file(files,fn)
+    res=files[fn]
+
+    if !res
+      files[fn]=[]
+      res=files[fn]
     end
-	  
+
+    return res
+  end
+
 end