seqtrimnext 2.0.51 → 2.0.52

data/lib/seqtrimnext/templates/amplicons.txt

@@ -9,18 +9,11 @@
 # Help: <ul>
 # Help: <li>PluginLowHighSize: rejecting too short or too long sequences</li>
 # Help: <li>PluginKey: trimming Roche 454 sequencing keys (typically 4 first nucleotides)</li>
-# Help: <li>PluginMids: trimming Roche 454 MIDs</li>
+# Help: <li>PluginMids: trimming Roche 454 MIDs and keys</li>
 # Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
 # Help: <li>PluginAbAdapters: trimming the Roche 454 AB adapters</li>
-# Help: <li>PluginAdapters: trimming the adapters found in SeqTrimNEXT database</li>
-# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
-# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
-# Help: <li>PluginFindPolyAt: trimming PolyA and PolyT. After a PolyT, the sequence is checked for low complexity. </li>
 # Help: <li>PluginAmplicons: getting sequences contained between two primers. Sequences with less than two primers are rejected. </li>
-# Help: <li>PluginLinker: splits Roche 454 paired-end sequences by any linker found in linkers database. Linker is removed.</li>
-# Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li>
 # Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
-# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
 # Help: </ul>
 
 plugin_list = PluginLowHighSize,PluginKey,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAmplicons,PluginLowQuality

data/lib/seqtrimnext/templates/genomics_454.txt

@@ -5,14 +5,18 @@
 # Help: <br/>This template is used to preprocess Roche 454 genomic data <br/>
 
 # Help: <br/><b>Plugin list and aplication order:</b><br/>
+
 # Help: <ul>
-# Help: <li>PluginLowHighSize</li>
-# Help: <li>PluginMids</li>
-# Help: <li>PluginIndeterminations</li>
-# Help: <li>PluginAbAdapters</li>
-# Help: <li>PluginContaminants</li>
-# Help: <li>PluginAmplicons</li>
-# Help: <li>PluginLowQuality</li>
+# Help: <li>PluginLowHighSize: rejecting too short or too long sequences</li>
+# Help: <li>PluginMids: trimming Roche 454 MIDs and keys</li>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+# Help: <li>PluginAbAdapters: trimming the Roche 454 AB adapters</li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
 # Help: </ul>
 
-plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginContaminants,PluginVectors,PluginLowQuality
+plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality

data/lib/seqtrimnext/templates/genomics_454_with_paired.txt

@@ -4,4 +4,22 @@
 
 # Help: <br/>This template is used to preprocess Roche 454 genomic data including paired-end <br/>
 
-plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginContaminants,PluginLinker,PluginVectors,PluginLowQuality
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
+
+# Help: <ul>
+# Help: <li>PluginLowHighSize: rejecting too short or too long sequences</li>
+# Help: <li>PluginMids: trimming Roche 454 MIDs and keys</li>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+# Help: <li>PluginAbAdapters: trimming the Roche 454 AB adapters</li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginLinker: splits Roche 454 paired-end sequences by any linker found in linkers database. Linker is removed.</li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: </ul>
+
+
+plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginUserContaminants,PluginContaminants,PluginLinker,PluginVectors,PluginLowQuality
+

data/lib/seqtrimnext/templates/genomics_short_reads.txt

@@ -3,5 +3,30 @@
 # ==============================================================
 
 # Help: <br/>This template is used to preprocess short reads for genomics <br/>
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
+
+# Help: <ul>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: </ul>
+
+plugin_list = PluginIndeterminations,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality
+
+generate_initial_stats = false
+
+# Minimum insert size for every trimmed sequence
+
+min_insert_size_trimmed = 30
+min_quality=20
+min_insert_size_trimmed=40
+min_insert_size_paired=40
+
+
+# do not remove cloned sequences
+remove_clonality=false
 
-plugin_list = PluginIndeterminations,PluginContaminants,PluginVectors,PluginLowQuality

data/lib/seqtrimnext/templates/genomics_short_reads_2.txt

@@ -3,5 +3,28 @@
 # ==============================================================
 
 # Help: <br/>This template is used to preprocess short reads for genomics including low complexity removal<br/>
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
+
+# Help: <ul>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li>
+# Help: </ul>
+
+plugin_list = PluginIndeterminations,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
+
+generate_initial_stats = false
+
+# Minimum insert size for every trimmed sequence
+
+min_insert_size_trimmed = 30
+
+
+# do not remove cloned sequences
+remove_clonality=false
 
-plugin_list = PluginIndeterminations,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity

data/lib/seqtrimnext/templates/only_quality.txt

@@ -0,0 +1,24 @@
+# ======================================
+# General parameters to extract Amplicons
+# ======================================
+
+# Help: <br/>This template is used to remove only bad quality regions<br/>
+
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
+
+# Help: <ul>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: </ul>
+
+plugin_list = PluginLowQuality
+
+# do not remove cloned sequences
+remove_clonality=false
+
+# remove amplicons containing less or equal number of sequences indicated
+
+generate_initial_stats = false
+
+# Minimum insert size for every trimmed sequence
+
+min_insert_size_trimmed = 30

data/lib/seqtrimnext/templates/sanger.txt

@@ -0,0 +1,25 @@
+# ======================================
+# General parameters SANGER
+# ======================================
+
+# Help: <br/>This template is used to preprocess Sanger genomic data <br/>
+
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
+
+# Help: <ul>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+# Help: <li>PluginAdapters: trimming adapters</li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: </ul>
+
+plugin_list = PluginIndeterminations,PluginAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality
+
+
+# do not remove cloned sequences
+remove_clonality=false
+

data/lib/seqtrimnext/templates/transcriptomics_454.txt

@@ -4,7 +4,24 @@
 
 # Help: <br/>This template is used to preprocess Roche 454 transcriptomic data <br/>
 
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
 
-plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
+# Help: <ul>
+# Help: <li>PluginLowHighSize: rejecting too short or too long sequences</li>
+# Help: <li>PluginMids: trimming Roche 454 MIDs and keys</li>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+# Help: <li>PluginAbAdapters: trimming the Roche 454 AB adapters</li>
+# Help: <li>PluginAdapters: trimming the adapters found in SeqTrimNEXT database</li>
+# Help: <li>PluginFindPolyAt: trimming PolyA and PolyT. After a PolyT, the sequence is checked for low complexity. </li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li>
+# Help: </ul>
+
+plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
 
 contaminants_db="contaminants.fasta cont_ribosome.fasta"

data/lib/seqtrimnext/templates/transcriptomics_plants.txt

@@ -3,7 +3,28 @@
 # ======================================
 
 # Help: <br/>This template is used to preprocess Roche 454 transcriptomic data. Customized for plants.<br/>
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
 
-plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
+# Help: <ul>
+# Help: <li>PluginLowHighSize: rejecting too short or too long sequences</li>
+# Help: <li>PluginMids: trimming Roche 454 MIDs and keys</li>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+# Help: <li>PluginAbAdapters: trimming the Roche 454 AB adapters</li>
+# Help: <li>PluginAdapters: trimming the adapters found in SeqTrimNEXT database</li>
+# Help: <li>PluginFindPolyAt: trimming PolyA and PolyT. After a PolyT, the sequence is checked for low complexity. </li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li>
+# Help: </ul>
+
+plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
 
 contaminants_db="contaminants.fasta cont_ribosome.fasta cont_mitochondrias.fasta cont_plastids.fasta"
+
+
+# do not remove cloned sequences
+remove_clonality=false

data/lib/seqtrimnext/templates/transcriptomics_short_reads.txt

@@ -3,7 +3,29 @@
 # ======================================
 
 # Help: <br/>This template is used to preprocess short reads for transcriptomics<br/>
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
 
-plugin_list = PluginIndeterminations,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
+# Help: <ul>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+# Help: <li>PluginFindPolyAt: trimming PolyA and PolyT. After a PolyT, the sequence is checked for low complexity. </li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li>
+# Help: </ul>
+
+plugin_list = PluginIndeterminations,PluginFindPolyAt,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
 
 contaminants_db="contaminants.fasta cont_ribosome.fasta"
+
+generate_initial_stats = false
+
+# Minimum insert size for every trimmed sequence
+
+min_insert_size_trimmed = 30
+
+# do not remove cloned sequences
+remove_clonality=false

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 = '2.0.51'
+   VERSION = '2.0.52'
   
   SEQTRIM_VERSION = VERSION
   

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 2.0.51
+  version: 2.0.52
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-06-20 00:00:00 Z
+date: 2012-07-16 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray
@@ -123,16 +123,27 @@ dependencies:
   type: :runtime
   version_requirements: *id010
 - !ruby/object:Gem::Dependency 
-  name: hoe
+  name: scbi_headers
   prerelease: false
   requirement: &id011 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.0.2
+  type: :runtime
+  version_requirements: *id011
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id012 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 2.8.0
   type: :development
-  version_requirements: *id011
+  version_requirements: *id012
 description: SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data. It makes use of scbi_mapreduce gem to be able to run in parallel and distributed environments. It is specially suited for Roche 454 (normal and paired-end) & Ilumina datasets, although it could be easyly adapted to any other situation.
 email: 
 - dariogf@gmail.com & alkoke@gmail.com
@@ -164,6 +175,8 @@ extensions: []
 extra_rdoc_files: 
 - History.txt
 - lib/seqtrimnext/templates/amplicons.txt
+- lib/seqtrimnext/templates/sanger.txt
+- lib/seqtrimnext/templates/only_quality.txt
 - lib/seqtrimnext/templates/genomics_454.txt
 - lib/seqtrimnext/templates/genomics_454_with_paired.txt
 - lib/seqtrimnext/templates/genomics_short_reads.txt
@@ -200,7 +213,7 @@ files:
 - lib/seqtrimnext/actions/action_ab_adapter.rb
 - lib/seqtrimnext/actions/action_ab_far_adapter.rb
 - lib/seqtrimnext/actions/action_ab_left_adapter.rb
-- lib/seqtrimnext/actions/action_classify.rb
+- lib/seqtrimnext/actions/action_user_contaminant.rb
 - lib/seqtrimnext/actions/action_empty_insert.rb
 - lib/seqtrimnext/actions/action_ignore_repeated.rb
 - lib/seqtrimnext/actions/action_indetermination.rb
@@ -251,7 +264,6 @@ files:
 - lib/seqtrimnext/plugins/plugin.rb
 - lib/seqtrimnext/plugins/plugin_ab_adapters.rb
 - lib/seqtrimnext/plugins/plugin_adapters.rb
-- lib/seqtrimnext/plugins/plugin_adapters_old.rb
 - lib/seqtrimnext/plugins/plugin_amplicons.rb
 - lib/seqtrimnext/plugins/plugin_contaminants.rb
 - lib/seqtrimnext/plugins/plugin_user_contaminants.rb
@@ -265,10 +277,11 @@ files:
 - lib/seqtrimnext/plugins/plugin_low_high_size.rb
 - lib/seqtrimnext/plugins/plugin_low_quality.rb
 - lib/seqtrimnext/plugins/plugin_mids.rb
-- lib/seqtrimnext/plugins/plugin_rem_adit_artifacts.rb
 - lib/seqtrimnext/plugins/plugin_short_insert.rb
 - lib/seqtrimnext/plugins/plugin_vectors.rb
 - lib/seqtrimnext/templates/amplicons.txt
+- lib/seqtrimnext/templates/sanger.txt
+- lib/seqtrimnext/templates/only_quality.txt
 - lib/seqtrimnext/templates/genomics_454.txt
 - lib/seqtrimnext/templates/genomics_454_with_paired.txt
 - lib/seqtrimnext/templates/genomics_short_reads.txt

data/lib/seqtrimnext/plugins/plugin_adapters_old.rb

@@ -1,165 +0,0 @@
-require "plugin"
-
-########################################################
-# Author: Almudena Bocinos Rioboo                      
-# 
-# Defines the main methods that are necessary to execute PluginAdapters                                                     
-# Inherit: Plugin
-########################################################
-
-class PluginAdaptersOld < 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
-  
- #Begins the plugin1's execution to warn that there are contaminants in the sequence "seq"
- 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 #{@params.get_param('adapters_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')}")  
-    $LOG.debug('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
-   
-    $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for adapters into the sequence" 
-  
-        
-    # blast=BatchBlast.new("-db #{File.join($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 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         
-    
-    adapters=[]
-    # blast_table_results.querys.each do |query|     # first round to save adapters without overlap
-      merge_hits(blast_query,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)
-        
-        # puts "action right end1 #{seq.insert_end}"
-        
-        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        
-        
-      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)  
-        
-    end 
-    seq.add_actions(actions)
-    #    
-  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 adapters or primers'
-    default_value = 1e-6
-		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='Path for adapter database'
-		default_value = File.join($FORMATTED_DB_PATH,'adapters.fasta')
-		params.check_param(errors,'adapters_db','DB',default_value,comment)		
-    
-    return errors
-  end
-  
-  
-end