seqtrimnext 2.0.39 → 2.0.41

data/History.txt

@@ -1,3 +1,13 @@
+=== 2.0.41 2011-11-04
+
+Added extra adapters plugin for transcriptomics
+
+=== 2.0.40 2011-10-27
+
+-Support Relative paths in user DB
+-Can mix relative and absolute paths in user DB
+-Custom linkers database
+
 === 2.0.39 2011-07-07
 
 Fixed database list option

data/Manifest.txt

@@ -41,6 +41,7 @@ lib/seqtrimnext/actions/action_poly_a.rb
 lib/seqtrimnext/actions/action_poly_t.rb
 lib/seqtrimnext/actions/action_rem_adit_artifacts.rb
 lib/seqtrimnext/actions/action_right_adapter.rb
+lib/seqtrimnext/actions/action_middle_adapter.rb
 lib/seqtrimnext/actions/action_right_primer.rb
 lib/seqtrimnext/actions/action_short_insert.rb
 lib/seqtrimnext/actions/action_unexpected_poly_t.rb

data/README.rdoc

@@ -118,15 +118,26 @@ The same way you can modify any of the parameters. You can find all parameters a
 == REQUIREMENTS:
 
 * Ruby 1.9.2
+* CD-HIT 4.5.3 or greater
 * Blast plus 2.24 or greater (prior versions have bugs that produces bad results)
 * [Optional] - GnuPlot version 4.4.2 or greater (prior versions may produce wrong graphs)
 * [Optional] - pdflatex - Optional, to produce a detailed report with results 
 
+
 == INSTALL:
 
+=== Installing CD-HIT
+
+*Download the latest version from http://code.google.com/p/cdhit/downloads/list
+*You can also use a precompiled version if you like
+*To install from source, decompress the downloaded file, cd to the decompressed folder, and issue the following commands:
+
+  make
+  sudo make install
+
 === Installing Blast
 
-*Download the latest version of Blast+ from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/
+*Download the latest version of Blast+ from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
 *You can also use a precompiled version if you like
 *To install from source, decompress the downloaded file, cd to the decompressed folder, and issue the following commands:
 

data/lib/seqtrimnext/actions/action_middle_adapter.rb

@@ -0,0 +1,29 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionMiddleAdapter < SeqtrimAction       
+  
+  def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+
+   end
+   
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class}. BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+#   
+# end  
+
+def apply_decoration(char)
+  return char.magenta
+end 
+
+end

data/lib/seqtrimnext/classes/params.rb

@@ -13,6 +13,7 @@ class Params
     # @param_order={}
     @mids = {}
     @ab_adapters={}
+    @adapters={}
     @linkers = {}
     @clusters = {}
 
@@ -55,17 +56,36 @@ class Params
     end
   end# end def
 
-  def load_db_fastas(path_file)
+  def load_db_fastas(input_paths)
+
     res={}
-    if File.exists?(path_file)
-      ff = FastaFile.new(path_file)
-      ff.each {|n,f|
-        # @mid_sizes[n]=f.size
-        res[n]=f
-      }
-
-      ff.close
+
+    if (!input_paths.nil?) & (input_paths!='')
+      # remove quotes
+      paths=input_paths.gsub(/\A['"]+|['"]+\Z/, "")
+
+      # split paths by spaces
+      # puts "PATHS:"
+      # puts paths.split(' ')
+      paths.split(' ').each do |path_file|
+
+        if File.exists?(path_file)
+          ff = FastaFile.new(path_file)
+          ff.each {|n,f|
+            res[n]=f
+          }
+
+          ff.close
+        end
+      end
+
     end
+
+    # puts "LOADED_DB #{paths}:"
+    # res.each do |k,v|
+    #   puts k
+    # end
+
     return res
   end
 
@@ -78,13 +98,19 @@ class Params
   # Load ab_adapters file
   def load_ab_adapters(path_file)
     @ab_adapters=load_db_fastas(path_file)
-        # puts @ab_adapters
+    # puts @ab_adapters
+  end
+
+  # load normal adapters
+  def load_adapters(path_file)
+    @adapters=load_db_fastas(path_file)
   end
 
+
   # Load mid's file
   def load_linkers(path_file)
     @linkers=load_db_fastas(path_file)
-        # puts @linkers
+    # puts @linkers
   end
 
   def load_repeated_seqs(file_path)
@@ -156,19 +182,38 @@ class Params
     return @params[param]
   end
 
+  def get_fasta(list,name,type)
+    res = list[name]
+    
+    if res.nil?
+      $LOG.error("Error. The #{type}: #{name} was not correctly loaded")
+      raise "Error. The #{type}: #{name} was not found in loaded #{name}s: #{list.map{|k,v| k}}."
+    end
+    
+    return res
+  end
+
   # Return the mid's size of param
-  def get_mid(param)
-    return @mids[param]
+  def get_mid(mid)
+    # return @mids[mid]
+    return get_fasta(@mids,mid,"mid")
   end
 
   # Return the linker of param
   def get_linker(linker)
-    return @linkers[linker]
+    # return @linkers[linker]
+    return get_fasta(@linkers,linker,"linker")
   end
 
   # Return the ab of param
   def get_ab_adapter(adapter)
-    return @ab_adapters[adapter]
+    # return @ab_adapters[adapter]
+    return get_fasta(@ab_adapters,adapter,"ab_adapter")
+  end
+
+  def get_adapter(adapter)
+    # return @adapters[adapter]
+    return get_fasta(@adapters,adapter,"adapter")
   end
 
 
@@ -300,16 +345,21 @@ class Params
                          # expand database paths
                          dbs= get_param(db_param_name).gsub('"','').split(/\s+/)
                          # puts "ALGO"*20
-                         puts dbs.join(',')
+                         # puts "INPUT DATABASES:\n"+dbs.join(',')
+
+                         procesed_dbs=[]
                          #
                          # TODO - chequear aqui que la db no esta vacia y que esta formateada.
-                         dbs.reverse_each {|db|
+                         dbs.reverse_each {|db_p|
+                           db=File.expand_path(db_p)
+
                            if !File.exists?(db)
-                             path=File.join($FORMATTED_DB_PATH,db)
+                             path=File.join($FORMATTED_DB_PATH,db_p)
                            else
                              path=db
                            end
 
+
                            if Dir.glob(path+'*.n*').entries.empty?
                              puts "DB file #{path} not formatted"
 
@@ -321,15 +371,19 @@ class Params
                              end
                            end
 
+                           procesed_dbs << path
+
                            if !File.exists?(path)
                              raise "DB File #{path} does not exists"
                              # exit
                            end
                          }
-                         db_paths = '"'+dbs.join(' ')+'"'
+
+                         db_paths = '"'+procesed_dbs.join(' ')+'"'
 
                          set_param(db_param_name,db_paths)
-                         # puts "DATABASES"+db_paths
+
+                         puts "USED DATABASES\n"+db_paths
                        end
   
   
@@ -351,7 +405,7 @@ class Params
                        end
   
   def check_param(errors,param,param_class,default_value=nil, comment=nil)
-                  
+
                          if !exists?(param)
                            if default_value.nil? #|| (default_value.is_a?(String) && default_value.empty?)
                              errors.push "The param #{param} is required and no default value is available"
@@ -360,41 +414,41 @@ class Params
                            end
                          end
 
-                           s = get_param(param)
+                         s = get_param(param)
 
 
-                           set_comment(get_plugin,param,comment)
+                         set_comment(get_plugin,param,comment)
 
-                           # check_class=Object.const_get(param_class)
-                           begin
+                         # check_class=Object.const_get(param_class)
+                         begin
 
-                             case param_class
-                             when 'Integer'
-                               r = Integer(s)
-                             when 'Float'
-                               r = Float(s)
-                             when 'String'
-                               r = String(s)
-                             when 'DB'
-                               # it is a string
-                               r = String(s)
-                               # and must be a valid db
-                               
-                               r = check_db_param(errors,param)
+                           case param_class
+                           when 'Integer'
+                             r = Integer(s)
+                           when 'Float'
+                             r = Float(s)
+                           when 'String'
+                             r = String(s)
+                           when 'DB'
+                             # it is a string
+                             r = String(s)
+                             # and must be a valid db
 
-                             when 'PluginList'
-                               r=String(s)
-                               r= check_plugin_list_param(errors,param)
-                             end
+                             r = check_db_param(errors,param)
 
-                           rescue Exception => e
-                             message="Current value is ##{s}#. "
-                             if param_class=='DB'
-                               message += e.message
-                             end
+                           when 'PluginList'
+                             r=String(s)
+                             r= check_plugin_list_param(errors,param)
+                           end
 
-                             errors.push "Param #{param} is not a valid #{param_class}. #{message}"
+                         rescue Exception => e
+                           message="Current value is ##{s}#. "
+                           if param_class=='DB'
+                             message += e.message
                            end
+
+                           errors.push "Param #{param} is not a valid #{param_class}. #{message}"
+                         end
                          # end
 
                        end

data/lib/seqtrimnext/classes/seqtrim.rb

@@ -230,14 +230,15 @@ class Seqtrim
       #MakeBlastDb.format_db(es.truncated_file_path,File.basename(es.truncated_file_path,File.extname(es.truncated_file_path)),'./') if piro_on
       
       # leer mids
-      params.load_mids(File.join($FORMATTED_DB_PATH,'mids.fasta'))
-      params.load_ab_adapters(File.join($FORMATTED_DB_PATH,'adapters_ab.fasta'))
-      params.load_linkers(File.join($FORMATTED_DB_PATH,'linkers.fasta'))
+      # params.load_mids(File.join($FORMATTED_DB_PATH,'mids.fasta'))
+      # params.load_ab_adapters(File.join($FORMATTED_DB_PATH,'adapters_ab.fasta'))
+      # params.load_linkers(File.join($FORMATTED_DB_PATH,'linkers.fasta'))
 
+      params.load_mids(params.get_param('mids_db'))
+      params.load_ab_adapters(params.get_param('adapters_ab_db'))
+      params.load_adapters(params.get_param('adapters_db'))
+      params.load_linkers(params.get_param('linkers_db'))
       
-      
-
-	    
       #execute cd-hit
       if params.get_param('remove_clonality')=='true'
         

data/lib/seqtrimnext/plugins/plugin.rb

@@ -71,7 +71,8 @@ class Plugin
 
   def merge_hits(hits,merged_hits,merged_ids=nil)
     # puts " merging ============"
-    hits.each do |hit|
+    # hits.each do |hit|
+    hits.sort{|h1,h2| (h1.q_end-h1.q_beg+1)<=>(h2.q_end-h2.q_beg+1)}.reverse_each do |hit|
 
       merged_ids.push hit.definition if !merged_ids.nil? && (! merged_ids.include?(hit.definition))
       # if new hit's position is already contained in hits, then ignore the new hit
@@ -86,20 +87,26 @@ class Plugin
         #contaminants.push({:q_begin=>hit.q_beg,:q_end=>hit.q_end,:name=>hit.subject_id})
         #
       else
-        # merge with old contaminant
-        min=[c.q_beg,hit.q_beg].min
-        max=[c.q_end,hit.q_end].max
 
-        c.q_beg=min
-        c.q_end=max
+        # one is inside each other, just ignore
+        if ((hit.q_beg>=c.q_beg && hit.q_end <=c.q_end) || (c.q_beg>=hit.q_beg && c.q_end <= hit.q_end))
+            # puts "* #{hit.subject_id} inside #{c.subject_id}"
+        else
+          # merge with old contaminant
+                      # puts "#{hit.subject_id} NOT inside #{c.subject_id}"
+          min=[c.q_beg,hit.q_beg].min
+          max=[c.q_end,hit.q_end].max
 
+          c.q_beg=min
+          c.q_end=max
 
-        # DONE para describir cada Id contaminante encontrado
-        # puts "1 -#{c.subject_id}-   -#{hit.subject_id}-"
-        c.subject_id += ' ' + hit.subject_id if (not c.subject_id.include?(hit.subject_id))
-        # puts "2 -#{c.subject_id}-   -#{hit.subject_id}-"
-        # puts "MERGE HIT (#{c.inspect})"
 
+          # DONE para describir cada Id contaminante encontrado
+          # puts "1 -#{c.subject_id}-   -#{hit.subject_id}-"
+          c.subject_id += ' ' + hit.subject_id if (not c.subject_id.include?(hit.subject_id))
+          # puts "2 -#{c.subject_id}-   -#{hit.subject_id}-"
+          # puts "MERGE HIT (#{c.inspect})"
+        end
         #
       end
 

data/lib/seqtrimnext/plugins/plugin_adapters.rb

@@ -9,41 +9,10 @@ require "plugin"
 
 class PluginAdapters < Plugin
   
-  def get_type_adapter(p_start,p_end,seq)
-       #if q_beg is nearer the left, add adapter action by the left,
-       #if q_end esta is nearer the right , add adapter action by  the right
-       #NOTE: If the adapter is very near from left and rigth,
-       #then the sequence isn't valid, because almost sequence is adapter.
-       
-       
-       v1= p_end.to_i
-       v2= p_start.to_i   
-       
-        # puts " startadapter #{v2} endadapter #{v1} insert_start #{seq.insert_start}  insert_end #{seq.insert_end}"
-       
-        # puts " #{v2+seq.insert_start} <? #{seq.seq_fasta.length - v1 - 1 + seq.seq_fasta_orig.length - seq.insert_end-1}"
-       if (v2+seq.insert_start  < (seq.seq_fasta.length - v1 - 1+ seq.seq_fasta_orig.length - seq.insert_end-1)) #IF THE NEAREST ONE IS THE LEFT
-         type = "ActionLeftAdapter"          
-         
-       else
-          type = "ActionRightAdapter"
-         
-       end
-       return type
-  end 
-  
-  
-  def cut_by_right(adapter,seq)
-    
-    left_size = adapter.q_beg-seq.insert_start+1
-    right_size = seq.insert_end-adapter.q_end+1
-    left_size=0 if (left_size<0)
-    right_size=0 if (right_size<0) 
-    
-    return (left_size>(right_size/2).to_i)
-    
-  end
-  
+  # adapters found at end of sequence are even 2 nt wide, cut in 5 because of statistics
+  MIN_ADAPTER_SIZE = 5
+  MIN_FAR_ADAPTER_SIZE = 13
+  # MIN_LEFT_ADAPTER_SIZE = 9
  #Begins the plugin1's execution to warn that there are contaminants in the sequence "seq"
  def execute(seqs)
    blasts= do_blasts(seqs)
@@ -55,7 +24,7 @@ class PluginAdapters < Plugin
  
  def do_blasts(seqs)
     # find MIDS  with less results than max_target_seqs value 
-    blast=BatchBlast.new("-db #{@params.get_param('adapters_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')}")  
+    blast=BatchBlast.new("-db #{@params.get_param('adapters_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_adapters')} -word_size #{MIN_ADAPTER_SIZE}")  
     $LOG.info('BLAST:'+blast.get_blast_cmd)
 
     fastas=[]
@@ -67,99 +36,179 @@ class PluginAdapters < Plugin
     
     # fastas=fastas.join("\n")
     
-    blast_table_results = blast.do_blast(fastas)
+    blast_table_results = blast.do_blast(fastas,:xml)
     
     # puts blast_table_results.inspect
    
     return blast_table_results
  end
  
+ # filter hits that are in the middle and do not have a valid length
+ def filter_hits(hits,end_pos)
+   
+   hits.reverse_each do |hit|
+    if (hit.q_beg>10) && (hit.q_end < (end_pos-10)) && ((hit.q_end-hit.q_beg+1)<(@params.get_adapter(hit.subject_id).length*0.85).to_i)
+      hits.delete(hit)
+      # puts "- DELETE #{hit.subject_id} #{(hit.q_end-hit.q_beg+1)}, < #{(@params.get_adapter(hit.subject_id).length*0.85).to_i} - R:#{hit.reversed}"
+      # 
+      # else
+      #   puts " ** ACCEPTED #{hit.subject_id} #{hit.q_beg}>6 and #{hit.q_end}<#{end_pos}-10, #{(hit.q_end-hit.q_beg+1)}, >= #{(@params.get_adapter(hit.subject_id).length*0.85).to_i} - R:#{hit.reversed}"
+      #   puts " *** #{hit.inspect}"
+    end
+   end
+   
+ 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.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for adapters into the sequence" 
   
         
-    # blast=BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'adapters.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')}")  
+    # blast=BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'adapters.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')} -word_size #{MIN_ADAPTER_SIZE}")  
+    
+    
     
     # blast with only one sequence, no with many sequences from a database
     #---------------------------------------------------------------------
     
     # blast_table_results = blast.do_blast(seq.seq_fasta)             #rise seq to adapterss  executing over blast
     
-    #blast_table_results = BlastTableResult.new(res) 
-    
-    # blast_table_results.inspect         
+     #BlastTableResult.new(res)
+     # puts blast_query.inspect
+     # puts blast_table_results.inspect
+     
+     filter_hits(blast_query.hits, seq.seq_fasta.length)
     
     adapters=[]
     # blast_table_results.querys.each do |query|     # first round to save adapters without overlap
-      merge_hits(blast_query,adapters)
+      merge_hits(blast_query.hits,adapters)
     # end
 
     begin 
       adapters2=adapters                            # second round to save adapters without overlap
       adapters = []
       merge_hits(adapters2,adapters)
-    end until (adapters2.count == adapters.count) 
-
-    actions=[] 
-    adapter_size=0
-    # @stats['adapter_size']={}
-    adapters.each do |ad|                           # adds the correspondent action to the sequence  
-       
-       type = get_type_adapter(ad.q_beg,ad.q_end,seq)
-       a = seq.new_action(ad.q_beg,ad.q_end,type) 
-       # puts " state left_action #{a.left_action} right_action #{a.right_action}"
-         
-
-       adapter_size=ad.q_end-ad.q_beg+1 
-       
-       if cut_by_right(ad,seq)
+    end until (adapters2.count == adapters.count)
+    
+    # puts "MERGED"
+    # puts "="*50
+    # adapters.each {|a| puts a.inspect}
+    
+    max_to_end=@params.get_param('max_adapters_to_end').to_i
+    # type = 'ActionAbAdapter'
+    actions=[]
+    adapter_size=0 
+    
+    #@stats['adapter_size']={}
+    adapters.each do |c|                           # adds the correspondent action to the sequence 
+      # puts "is the adapter near to the end of sequence ? #{c.q_end+seq.insert_start+max_to_end} >= ? #{seq.seq_fasta_orig.size-1}"   
+        adapter_size=c.q_end-c.q_beg+1
+        #if ((c.q_end+seq.insert_start+max_to_end)>=seq.seq_fasta_orig.size-1)  
+        right_action = true
         
-        # puts "action right end1 #{seq.insert_end}"
+        #if ab adapter is very near to the end of original sequence
+	      if c.q_end>=seq.seq_fasta.length-max_to_end
+          # message = c.subject_id
+          message = c.definition
+          type = 'ActionRightAdapter'
+          ignore=false 
+          add_stats('adapter_type','right')
         
-        a.right_action=true    #mark rigth action to get the left insert
-      else 
-          
-        # puts " cut1 by left #{seq.insert_start} ad #{ad.q_beg+seq.insert_start} #{ad.q_end+seq.insert_start}"
-                 
-        a.left_action = true   #mark left action to get the right insert        
+        elsif (c.q_beg <= 6) #&& (adapter_size>=MIN_LEFT_ADAPTER_SIZE) #left adapter
+          # message = c.subject_id    
+          message = c.definition
+          type = 'ActionLeftAdapter'
+          ignore = false
+          right_action = false
+          add_stats('adapter_type','left')
+        elsif (adapter_size>=MIN_FAR_ADAPTER_SIZE)
+          # message = c.subject_id    
+          message = c.definition
+          type = 'ActionMiddleAdapter'
+          ignore = false
+          add_stats('adapter_type','middle')
+        else
+          ignore=true 
+        end 
         
-      end 
-      
-      a.message = ad.subject_id 
-      a.reversed = ad.reversed 
-      actions.push a 
-      
-      # @stats[:adapter_size]={adapter_size => 1} 
-      add_stats('adapter_size',adapter_size)  
+        if !ignore
+          a = seq.new_action(c.q_beg,c.q_end,type) 
+          a.message = message 
+          a.reversed = c.reversed 
+          if right_action
+            a.right_action = true    #mark as rigth action to get the left insert
+          else
+            a.left_action = true
+          end
+          actions.push a  
         
+          # puts "adapter_size #{adapter_size}"
+
+          #@stats[:adapter_size]={adapter_size => 1} 
+          add_stats('adapter_size',adapter_size) 
+          add_stats('adapter_id',message)
+        end 
     end 
-    seq.add_actions(actions)
+    
+    if !actions.empty?
+      seq.add_actions(actions)   
+      add_stats('sequences_with_adapter','count')
+    end
+    
+    
     #    
   end
 
   #Returns an array with the errors due to parameters are missing 
   def self.check_params(params)
-    errors=[]
+    errors=[]  
     
-    comment='Blast E-value used as cut-off when searching for adapters or primers'
-    default_value = 1e-6
+    comment='Blast E-value used as cut-off when searching for adapters'
+    # default_value = 1e-6
+		default_value = 1
 		params.check_param(errors,'blast_evalue_adapters','Float',default_value,comment)
 		
 		comment='Minimum required identity (%) for a reliable adapter'
 		default_value = 95
 		params.check_param(errors,'blast_percent_adapters','Integer',default_value,comment)
+		
+    comment='Adapters can be found at both ends of the sequence. The following variable indicates the number of nucleotides that are allowed for considering the adapters to be located at the right end'
+		default_value = 9
+		params.check_param(errors,'max_adapters_to_end','Integer',default_value,comment)
     
-    comment='Path for adapter database'
+    comment='Path for adapters database'
 		default_value = File.join($FORMATTED_DB_PATH,'adapters.fasta')
-		params.check_param(errors,'adapters_db','DB',default_value,comment)		
+		params.check_param(errors,'adapters_db','DB',default_value,comment)
     
     return errors
   end
   
+  def self.get_graph_title(plugin_name,stats_name)
+    case stats_name
+    when 'adapter_type'
+      'Adapters by type'
+    when 'adapter_size'
+      'Adapters by size'
+    end
+  end
+
+  def self.get_graph_filename(plugin_name,stats_name)
+    return stats_name
+    
+    # case stats_name
+    # when 'adapter_type'
+    #   'AB adapters by type'
+    # when 'adapter_size'
+    #   'AB adapters by size'
+    # end
+  end
+  
+  def self.valid_graphs
+    return ['adapter_type']
+  end
+
   
 end

data/lib/seqtrimnext/plugins/plugin_linker.rb

@@ -81,7 +81,7 @@ class PluginLinker < Plugin
 
   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)
 
@@ -223,6 +223,10 @@ class PluginLinker < Plugin
 		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

data/lib/seqtrimnext/templates/transcriptomics_454.txt

@@ -3,6 +3,6 @@
 # ======================================
 
 
-plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
+plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
 
 contaminants_db="contaminants.fasta cont_ribosome.fasta"

data/lib/seqtrimnext.rb

@@ -30,7 +30,7 @@ module Seqtrimnext
   # SEQTRIM_VERSION_STAGE = 'b'
   # SEQTRIM_VERSION = "2.0.0#{SEQTRIM_VERSION_STAGE}#{SEQTRIM_VERSION_REVISION}"
   
-   VERSION = '2.0.39'
+   VERSION = '2.0.41'
   
   SEQTRIM_VERSION = VERSION
   

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 2.0.39
+  version: 2.0.41
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-07-07 00:00:00 Z
+date: 2011-11-07 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray
@@ -214,6 +214,7 @@ files:
 - lib/seqtrimnext/actions/action_poly_t.rb
 - lib/seqtrimnext/actions/action_rem_adit_artifacts.rb
 - lib/seqtrimnext/actions/action_right_adapter.rb
+- lib/seqtrimnext/actions/action_middle_adapter.rb
 - lib/seqtrimnext/actions/action_right_primer.rb
 - lib/seqtrimnext/actions/action_short_insert.rb
 - lib/seqtrimnext/actions/action_unexpected_poly_t.rb