seqtrimnext 2.0.29

data/lib/seqtrimnext/plugins/plugin_key.rb

@@ -0,0 +1,70 @@
+require "plugin"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginKey                                                     
+# Inherit: Plugin
+########################################################
+
+class PluginKey < Plugin   
+  
+  
+   #Begins the pluginKey's execution to warn where is a key in the sequence "seq"    
+  def execute(seqs)
+     @group_by_key=(@params.get_param('use_independent_folder_for_each_key')=='true')
+     
+     seqs.each do |s|
+         exec_seq(s)
+     end
+   end
+
+
+   def exec_seq(seq)
+     $LOG.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: marking key into the sequence" 
+     # blast_table_results.inspect        
+     
+     actions=[]
+     
+     key_size=0
+     # mid_size=0
+     key_beg,key_end=[0,3]
+     key_size=4
+     key=seq.seq_fasta[0..3].upcase
+     
+     a = seq.new_action(key_beg,key_end,'ActionKey') # adds the actionKey to the sequence
+     actions.push a       
+     
+     #Add actions  
+     seq.add_actions(actions)
+     
+     
+     if @group_by_key
+       
+       seq.add_file_tag(0,'key_' + key, :dir)
+       add_stats('key_tag',key)
+     end
+     
+     add_stats('key_size',key_size)
+     # add_stats('mid_size',mid_size)
+           
+
+     
+   end
+ 
+  #Returns an array with the errors due to parameters are missing 
+  def self.check_params(params)
+    errors=[]
+    
+    # self.check_param(errors,params,'blast_evalue_mids','Float')
+    # self.check_param(errors,params,'blast_percent_mids','Integer')
+    comment='sequences containing with diferent keys (barcodes) are saved to separate folders'
+	  default_value='false'
+	  params.check_param(errors,'use_independent_folder_for_each_key','String',default_value,comment)
+    
+    
+    return errors
+  end
+  
+  
+end

data/lib/seqtrimnext/plugins/plugin_linker.rb

@@ -0,0 +1,232 @@
+require "plugin"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginLinker                                                     
+# Inherit: Plugin
+########################################################
+class PluginLinker < Plugin
+  MAX_LINKER_ERRORS=2
+  #-------------------------------------------------------------------------
+  #It's created an ActionInsert or ActionShortInsert before the ActionLinker 
+  #Used: in class PluginLinker and PluginMid
+  #-------------------------------------------------------------------------
+  # def add_action_before_linker(p_q_beg,size_insert,actions,seq)
+  # 
+  #    size_min_insert = @params.get_param('size_min_insert').to_i
+  #    if ((p_q_beg>0) && (size_insert>=size_min_insert))         #if linker's positions are right    
+  #       #It's created an ActionInsert or ActionShortInsert before the ActionLinker    
+  #       a = seq.new_action(0,p_q_beg-1,"ActionInsert") # adds the ActionInsert to the sequence before adding the actionMid
+  #       actions.push a
+  #    elsif (p_q_beg>0)  #if linker's positions are right and insert's size is short
+  #      #It's created an ActionShortInsert before the ActionLinker
+  #      a = seq.new_action(0,p_q_beg-1,"ActionShortInsert") # adds the ActionInsert to the sequence before adding the actionMid
+  #       actions.push a 
+  #    end
+  #    
+  #  end  
+  
+  #-------------------------------------------------------------------------
+  #It's created an ActionInsert or ActionShortInsert after the ActionLinker 
+  #-------------------------------------------------------------------------
+  # def add_action_after_linker(p_q_end,size_insert,actions,seq) 
+  #   
+  #   size_min_insert = @params.get_param('size_min_insert').to_i     
+  # 
+  #   if ((p_q_end<seq.seq_fasta.size-1) && (size_insert>=size_min_insert) )  #if linker's positions are right 
+  #     #It's created an ActionInsert after the ActionLinker
+  #     a = seq.new_action(p_q_end+1,seq.seq_fasta.size-1,"ActionInsert") # adds the ActionInsert to the sequence before adding the actionMid
+  # 
+  #     actions.push a
+  #       
+  #   elsif (p_q_end<seq.seq_fasta.size-1)   #if linker's positions are right and insert's size is short 
+  #     #It's created an ActionInsert after the ActionLinker
+  #     a = seq.new_action(p_q_end+1,seq.seq_fasta.size-1,"ActionShortInsert") # adds the ActionInsert to the sequence before adding the actionMid
+  # 
+  #     actions.push a 
+  #   end
+  #   
+  # end
+  # 
+  
+  def sum_quals(a)
+	  	res = 0
+	  	
+	  	a.map{|e| res+=e}
+	  	
+		return res
+  end
+  
+  def merge_hits_with_same_qbeg_and_qend(hits)
+	  	res =[]
+  
+  		hits.each do |hit|
+				if !res.find{|h| (h.q_beg==hit.q_beg) && (h.q_end==hit.q_end)}
+					res.push hit
+				end
+  		end  
+
+  		return res
+  end
+ 
+  # Begins the plugin1's execution to warn that there is linker  into the sequence
+  def execute(seqs)
+    blasts= do_blasts(seqs)
+
+    seqs.each_with_index do |s,i|
+      exec_seq(s,blasts.querys[i])
+    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          
+
+     $LOG.info('BLAST:'+blast.get_blast_cmd)
+
+     fastas=[]
+
+     seqs.each do |seq|
+      fastas.push ">"+seq.seq_name
+      fastas.push seq.seq_fasta
+     end
+
+     # fastas=fastas.join("\n")
+
+     blast_table_results = blast.do_blast(fastas)
+
+     # puts blast_table_results.inspect
+
+     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}"
+    end
+     $LOG.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for linker into the sequence"
+     
+     # key_beg,key_end=search_key(seq,0,3)   if false       
+     # blast = BatchBlast.new("-subject #{File.join($FORMATTED_DB_PATH,'linkers.fasta')}",'blastn'," -task blastn  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers
+     # 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_table_results = blast.do_blast(seq.seq_fasta)             #rise seq to linkers  executing over blast 
+    
+
+     #blast_table_results = BlastTableResult.new(res) 
+     actions=[]  
+     linker_size=0
+          
+     if (!blast_query.hits.empty?) #linker found
+     
+			linkers = merge_hits_with_same_qbeg_and_qend(blast_query.hits)
+
+			if linkers.count ==1
+			
+         linker=linkers.first
+         
+         linker_size=linker.q_end-linker.q_beg+1
+		     
+		     if (linker.gaps+linker.mismatches>MAX_LINKER_ERRORS) # number of ERRORS and GAPs is higher than MAX_LINKER_ERRORS, 
+		         seq.seq_rejected=true
+		         seq.seq_rejected_by_message='linker with mismatches'
+		         # @stats[:rejected_seqs]={'rejected_seqs_by_errors' => 1}
+		         add_stats('rejected','by_linker_errors')
+			 		   add_stats('linker_errors',linker.gaps+linker.mismatches)
+		     else     
+		       #Create an ActionLinker
+		        a = seq.new_action(linker.q_beg,linker.q_end,'ActionLinker') # adds the ActionLinker to the sequence 
+		        a.message = linker.subject_id 
+		        a.tag_id = linker.subject_id
+		        actions.push a  
+		        
+            # seq.add_file_tag(0, 'paired', :file)
+		        
+		        add_stats('linker_id',linker.subject_id)
+		        add_stats('linker_id','total')
+		        
+		     end
+		     
+			else # multiple linkers found
+			  q_begs=[]
+			  q_ends=[]
+
+			  linker_count=linkers.count
+			  
+				linkers.each do |linker|
+					#puts "*MULTILINKER* #{linker.subject_id[0..40].ljust(40)} #{linker.q_beg.to_s.rjust(6)} #{linker.q_end.to_s.rjust(6)} #{linker.s_beg.to_s.rjust(6)} #{linker.s_end.to_s.rjust(6)}"
+					q_begs.push linker.q_beg
+					q_ends.push linker.q_end
+
+				end
+       		
+     		first_linker = linkers.first
+     		last_linker = linkers.last
+       	
+   		  a = seq.new_action(q_begs.min,q_ends.max,'ActionMultipleLinker') # adds the ActionLinker to the sequence
+        a.message = "#{linker_count} x #{first_linker.subject_id}"
+        a.tag_id = first_linker.subject_id
+        
+        #determine with part (left or right) has the best quality
+        left_quals = seq.seq_qual[0,q_begs.min]
+			  sum_left=sum_quals(left_quals)
+        
+        right_quals = seq.seq_qual[q_ends.max+1..seq.seq_qual.length]
+        sum_right=sum_quals(right_quals)
+        
+        if sum_left>=sum_right
+	        a.right_action=true
+	      else
+	      		a.left_action=true
+	      	end
+        
+        #puts "SUM QUAL LEFT:#{sum_left} count:#{left_quals.length}"
+        #puts "SUM QUAL RIGHT:#{sum_right} count:#{right_quals.length}"
+        
+        
+        actions.push a
+        
+        add_stats('multiple_linker_id',first_linker.subject_id)
+        add_stats('multiple_linker_id','total')
+        add_stats('multiple_linker_count',linker_count)
+        
+#				puts "=== > seq_qual: #{seq.seq_qual.count}"
+#        seq.get_qual_inserts.each do |qi|
+#        		puts "==> #{qi.join(' ')}"
+#        end
+
+  			end
+  			
+  		else # no linker found
+	  		add_stats('without_linker',linker_size)
+    end
+	    
+	    
+    if !actions.empty?
+		  #Add actions
+		  seq.add_actions(actions)
+	  end
+
+  end
+ 
+  
+  #Returns an array with the errors due to parameters are missing 
+  def self.check_params(params)
+    errors=[]  
+    
+    comment='Blast E-value used as cut-off when searching for linkers in paired-ends'
+		default_value = 1e-10
+		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)
+		
+    
+    return errors
+  end
+  
+  
+end

data/lib/seqtrimnext/plugins/plugin_low_complexity.rb

@@ -0,0 +1,98 @@
+########################################################
+# Author: Almudena Bocinos Rioboo
+#
+# Defines the main methods that are necessary to execute PluginLowComplexity
+
+#
+# Inherit: Plugin
+########################################################
+
+require "plugin"
+
+MIN_DUST_SIZE = 30
+
+class PluginLowComplexity < Plugin
+
+
+
+  def execute(seqs)
+    dust= do_dust(seqs)
+    
+    seqs.each_with_index do |s,i|
+      exec_seq(s,dust[i])
+    end
+  end
+  
+  def do_dust(seqs)
+     # find MIDS  with less results than max_target_seqs value 
+     dust_masker=DustMasker.new()
+
+     fastas=[]
+     
+     seqs.each do |seq|
+      fastas.push ">"+seq.seq_name
+      fastas.push seq.seq_fasta
+     end
+     
+     # fastas=fastas.join("\n")
+     
+     found_dust = dust_masker.do_dust(fastas)
+     # puts found_dust
+     # puts blast_table_results.inspect
+    
+     return found_dust
+  end
+  
+  
+  def exec_seq(seq,dust_query)
+    if dust_query.query_id != seq.seq_name
+      raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
+    end
+    actions=[]
+
+      # puts "Checking for dust: #{seq.seq_fasta}"
+      # puts found_dust.to_json
+      total_dust=0
+      if !dust_query.nil?
+        dust_query.dust.each do |dust|
+          start=dust[0]
+          stop=dust[1]
+          dust_size=dust[1]-dust[0]+1
+          total_dust+=dust_size
+
+          if (dust_size)>=MIN_DUST_SIZE
+          
+            a = seq.new_action(start,stop,'ActionLowComplexity')
+            # a.left_action=true
+            actions.push a
+            # break
+          end
+        end
+      end
+      
+      if !actions.empty?
+        add_stats('low_complexity',total_dust)
+        seq.add_actions(actions)
+      end
+
+  end
+
+
+
+  ######################################################################
+  #---------------------------------------------------------------------
+
+  #Returns an array with the errors due to parameters are missing
+  def self.check_params(params)
+    errors=[]
+
+    # 
+    # comment='Minimum percent of T bases in poly_a to be accepted'
+    # default_value = 80
+    # params.check_param(errors,'poly_t_percent','Integer',default_value,comment)
+    # 
+    return errors
+  end
+
+
+end

data/lib/seqtrimnext/plugins/plugin_low_high_size.rb

@@ -0,0 +1,74 @@
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginLowHighSize
+
+#                                                     
+# Inherit: Plugin
+########################################################
+require "plugin"
+
+
+class PluginLowHighSize < Plugin
+  
+  
+ # Begins the plugin_low_high_size's execution with the sequence "seq"
+ 
+ def execute(seqs)
+   seqs.each do |s|
+       exec_seq(s)
+    end
+  end
+  
+  
+  def exec_seq(seq)   
+    $LOG.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: checking low or high size of the sequence"    
+    
+    min_size = @params.get_param('min_sequence_size_raw').to_i #min_size is: mean - 2dev
+    max_size = @params.get_param('max_sequence_size_raw').to_i #max_size is: mean + 2dev
+    #add_stats('rejected_seqs',seq.seq_fasta.length)
+    actions=[]
+
+    if ((seq.seq_fasta.length>max_size) || (seq.seq_fasta.length<min_size))  #if length of sequence is out of (-2dev,2dev)
+      $LOG.debug "#{seq.seq_name} rejected by size #{seq.seq_fasta.length} "
+      type='ActionLowHighSize'
+      # seq.add_action(0,seq.seq_fasta.length,type)  
+      a = seq.new_action(0,seq.seq_fasta.length,type)
+      a.message = 'low or high size'
+      seq.seq_rejected = true 
+      seq.seq_rejected_by_message= 'size out of limits'
+       
+      add_stats('rejected_seqs',seq.seq_fasta.length)    
+      actions.push a
+      seq.add_actions(actions)
+    
+    end  
+    
+    
+  end
+  
+  ######################################################################
+  #---------------------------------------------------------------------
+  
+ 
+
+  ######################################################################
+  #---------------------------------------------------------------------
+
+  #Returns an array with the errors due to parameters are missing 
+  def self.check_params(params)
+    errors=[]
+    
+    comment='Minimum size for a raw input sequence to be analysed (shorter reads are directly rejected without further analysis)'
+		default_value = 40
+		params.check_param(errors,'min_sequence_size_raw','Integer',default_value,comment)
+
+    #self.check_param(errors,params,'max_sequence_size_raw','Integer')
+    
+    
+    return errors
+  end
+  
+
+  
+end