seqtrimnext 2.0.54 → 2.0.55

checksums.yaml

@@ -0,0 +1,7 @@
+--- 
+SHA1: 
+  metadata.gz: 986a3873d8d82691a22f08f33859fc93859d0339
+  data.tar.gz: 09efc77da8b82592df05056af9a1aeda4909d6a3
+SHA512: 
+  metadata.gz: bb5158b002d5847daf8c968c74da3fa120375ba7527abbb5c6397601b491db78a4416671fd5626fcf5821114613f175cd714866b154e2622067cd1f60c4abbc9
+  data.tar.gz: 0a44e613a6195480e69ff5d9298ad5b786e732748a03b5a7c2732d046c3c022c27af6d0d110cbbff885f907fe8e983d5f1f4261558dae074f48183d5b70d2746

data/History.txt

@@ -1,6 +1,10 @@
+=== 2.0.55 2013-07-23
+
+Sanger adapters plugin. Option to disable reject by indeterminations in the middle of a sequence.
+
 === 2.0.54 2012-09-07
 
-Write fastq as  fastq.gz
+* Flag to write fastq files as fastq.gz
 
 === 2.0.53 2012-07-24
 

data/Manifest.txt

@@ -18,12 +18,15 @@ bin/resume_rejected.rb
 bin/reverse_paired.rb
 bin/seqtrimnext
 bin/split_fastq.rb
+bin/split_fasta.rb
 bin/split_ilumina_paired.rb
 bin/split_paired.rb
 History.txt
 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_sanger_left_adapter.rb
+lib/seqtrimnext/actions/action_sanger_right_adapter.rb
 lib/seqtrimnext/actions/action_user_contaminant.rb
 lib/seqtrimnext/actions/action_empty_insert.rb
 lib/seqtrimnext/actions/action_ignore_repeated.rb
@@ -74,6 +77,7 @@ lib/seqtrimnext/classes/sequence_group.rb
 lib/seqtrimnext/classes/sequence_with_action.rb
 lib/seqtrimnext/plugins/plugin.rb
 lib/seqtrimnext/plugins/plugin_ab_adapters.rb
+lib/seqtrimnext/plugins/plugin_sanger_adapters.rb
 lib/seqtrimnext/plugins/plugin_adapters.rb
 lib/seqtrimnext/plugins/plugin_amplicons.rb
 lib/seqtrimnext/plugins/plugin_contaminants.rb
@@ -99,7 +103,7 @@ lib/seqtrimnext/templates/genomics_short_reads.txt
 lib/seqtrimnext/templates/genomics_short_reads_2.txt
 lib/seqtrimnext/templates/transcriptomics_454.txt
 lib/seqtrimnext/templates/transcriptomics_short_reads.txt
-lib/seqtrimnext/templates/transcriptomics_plants.txt
+lib/seqtrimnext/templates/transcriptomics_454_plants.txt
 lib/seqtrimnext/utils/extract_samples.rb
 lib/seqtrimnext/utils/fasta2xml.rb
 lib/seqtrimnext/utils/global_match.rb
@@ -118,4 +122,4 @@ script/console
 script/destroy
 script/generate
 test/test_helper.rb
-test/test_seqtrimnext.rb
+test/test_seqtrimnext.rb

data/bin/seqtrimnext

@@ -141,11 +141,11 @@ def show_additional_help
 
   puts "\n"*3
   puts "E.g.: processing a fastq sequences file"
-  puts "#{$0} -t genomics_454.txt -Q sequences.fastq"
+  puts "#{File.basename($0)} -t genomics_454.txt -Q sequences.fastq"
   puts "\n"*2
 
   puts "E.g.: processing a fasta file with qual"
-  puts "#{$0} -t genomics_454.txt -f sequences.fasta -q sequences.qual"
+  puts "#{File.basename($0)} -t genomics_454.txt -f sequences.fasta -q sequences.qual"
 
   templates = Dir.glob(File.join($SEQTRIM_PATH,'templates','*.txt')).map{|t| File.basename(t)}
 

data/bin/split_fasta.rb

@@ -0,0 +1,45 @@
+#!/usr/bin/env ruby
+
+require 'scbi_fasta'
+
+
+if ARGV.count < 3
+  puts "#{$0} FASTA_FILE OUTPUT_NAME SEQS_PER_FILE_COUNT"
+  exit
+end
+
+
+  
+fastq = ARGV.shift
+output_name = ARGV.shift
+split_by = ARGV.shift.to_i
+
+
+file_index=1
+out=File.new("#{output_name}#{file_index}.fasta",'w')
+
+fqr=FastaQualFile.new(fastq)
+
+count = 0
+
+fqr.each do |seq_name,seq_fasta,comments|
+  
+
+  out.puts(">#{seq_name+i.to_s} #{comments}")
+  out.puts(seq_fasta)
+
+  count +=1
+
+  if (count % split_by) == 0 
+      
+    file_index +=1
+    out.close
+    out=File.new("#{output_name}#{file_index}.fasta",'w')
+
+  end
+end
+
+ 
+out.close
+fqr.close
+

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 = '2.0.54'
+   VERSION = '2.0.55'
   
   SEQTRIM_VERSION = VERSION
   

data/lib/seqtrimnext/actions/action_sanger_left_adapter.rb

@@ -0,0 +1,31 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionSangerLeftAdapter < 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.negative
+  
+  #  return char.magenta.negative
+end  
+
+end

data/lib/seqtrimnext/actions/action_sanger_right_adapter.rb

@@ -0,0 +1,32 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionSangerRightAdapter < 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.negative
+  
+  #  return char.magenta.negative
+end  
+
+
+end

data/lib/seqtrimnext/plugins/plugin_indeterminations.rb

@@ -100,9 +100,11 @@ class PluginIndeterminations < Plugin
 		      a.right_action=true
 		      actions.push a
 		  
-		      seq.seq_rejected=true 
-          seq.seq_rejected_by_message='Indeterminations in middle of sequence'
-		  
+          if @params.get_param('middle_indetermination_rejects')=='true'
+		        seq.seq_rejected=true 
+            seq.seq_rejected_by_message='Indeterminations in middle of sequence'
+          end
+		      
 		      poly_size=poly['end']-poly['begin']+1
 		      add_stats('size',poly_size)
 	      end
@@ -180,9 +182,13 @@ class PluginIndeterminations < Plugin
 		default_value = 80
 		params.check_param(errors,'poly_n_percent','Integer',default_value,comment)
 
- 		comment='Maximum distance to the end of the sequence to be considered an internal segment'
-		default_value = 15
-		params.check_param(errors,'poly_n_max_to_end','Integer',default_value,comment)
+    comment='Maximum distance to the end of the sequence to be considered an internal segment'
+    default_value = 15
+    params.check_param(errors,'poly_n_max_to_end','Integer',default_value,comment)
+
+ 		comment='Rejects sequences with indeterminations in the middle'
+		default_value = 'true'
+		params.check_param(errors,'middle_indetermination_rejects','String',default_value,comment)
     
     return errors
   end

data/lib/seqtrimnext/plugins/plugin_sanger_adapters.rb

@@ -0,0 +1,227 @@
+require "plugin"
+
+########################################################
+# Author: DGF y ABR                      
+# 
+# Defines the main methods that are necessary to execute PluginAdapters                                                     
+# Inherit: Plugin
+########################################################
+
+class PluginSangerAdapters < Plugin
+  
+  # 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
+ 
+ def do_blasts(seqs)
+    
+    # find MIDS  with less results than max_target_seqs value 
+    blast=BatchBlast.new("-db #{@params.get_param('adapters_sanger_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_sanger')} -word_size #{MIN_ADAPTER_SIZE}")  
+    $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
+ 
+ # filter hits that are far the extreme and do not have a valid length
+ def filter_hits(hits,end_pos)
+   # hits.reverse_each do |hit|
+   #  # if (hit.q_end < (end_pos-40)) && ((hit.q_end-hit.q_beg+1)<(@params.get_sanger_adapter(hit.subject_id).length*0.80).to_i)
+   #  if ((hit.q_end-hit.q_beg+1)<(@params.get_sanger_adapter(hit.subject_id).length*0.80).to_i)
+   #    hits.delete(hit)
+   #  end
+   # end
+   
+ end
+
+ def filter_adapters(adapters)
+
+  min_size=@params.get_param('min_sanger_adapter_size').to_i
+  adapters.reverse_each do |c|
+    adapter_size=c.q_end-c.q_beg+1
+
+    if adapter_size < min_size
+      adapters.delete(c)
+    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}"
+   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_ab.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_ab')} -perc_identity #{@params.get_param('blast_percent_ab')} -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
+    
+     #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.hits,adapters)
+    # end
+
+    begin 
+      adapters2=adapters                            # second round to save adapters without overlap
+      adapters = []
+      merge_hits(adapters2,adapters)
+    end until (adapters2.count == adapters.count)
+
+    # type = 'ActionAbAdapter'
+    actions=[]   
+    adapter_size=0 
+
+    filter_adapters(adapters)
+
+    if adapters.count==1 # only one adapter
+      c=adapters.first
+      adapter_size=c.q_end-c.q_beg+1
+      message = c.subject_id 
+      type = 'ActionSangerLeftAdapter'
+      stat_type='left'
+      add_stats('adapter_type',stat_type)
+
+      a = seq.new_action(c.q_beg,c.q_end,type)
+      a.message = message 
+      a.reversed = c.reversed 
+      a.left_action = true
+      actions.push a
+             
+      add_stats('adapter_size',adapter_size) 
+      add_stats('adapter_id',message)
+
+    elsif adapters.count >=2
+      type = 'ActionSangerLeftAdapter'
+      stat_type='left'
+      left_action=true
+      right_action=false
+
+      adapters.sort!{|a1,a2| a1.q_beg <=> a2.q_beg}
+      old_qend=adapters.first.q_end
+      
+      max_slice_size=[]
+
+      # left_qend=adapters.first.q_end
+      adapters.each do |c|                           # adds the correspondent action to the sequence 
+
+
+        # check if it is a right adapter
+        if c.q_beg > (old_qend+50)
+          type=type = 'ActionSangerRightAdapter'
+          stat_type='right'
+          left_action=false
+          right_action=true
+        end
+
+        adapter_size=c.q_end-c.q_beg+1
+        message = c.subject_id 
+        add_stats('adapter_type',stat_type)
+
+        a = seq.new_action(c.q_beg,c.q_end,type)
+        a.message = message 
+        a.reversed = c.reversed 
+        a.left_action = left_action
+        a.right_action = right_action
+
+        # if action.last.q_end - a.start_pos > max_slice_size.last[:size]
+        
+        # end
+
+        actions.push a
+      
+        add_stats('adapter_size',adapter_size)
+        add_stats('adapter_id',message)
+
+        old_qend=adapters.first.q_end
+
+      end
+      
+    end    
+    
+    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=[]  
+    
+    comment='Blast E-value used as cut-off when searching for Sanger adapters'
+    # default_value = 1e-6
+    default_value = 1
+    params.check_param(errors,'blast_evalue_sanger','Float',default_value,comment)
+    
+    comment='Minimum required identity (%) for a reliable Sanger adapter'
+    default_value = 95
+    params.check_param(errors,'blast_percent_sanger','Integer',default_value,comment)
+
+    comment='Minimum required adapter size for a valid Sanger adapter'
+    default_value = 10
+    params.check_param(errors,'min_sanger_adapter_size','Integer',default_value,comment)
+    
+    comment='Path for Sanger adapters database'
+    default_value = File.join($FORMATTED_DB_PATH,'adapters_sanger.fasta')
+    params.check_param(errors,'adapters_sanger_db','DB',default_value,comment)
+    
+    return errors
+  end
+  
+  def self.get_graph_title(plugin_name,stats_name)
+    case stats_name
+    when 'adapter_type'
+      'Sanger adapters by type'
+    when 'adapter_size'
+      'Sanger 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/templates/sanger.txt

@@ -17,7 +17,7 @@
 # Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
 # Help: </ul>
 
-plugin_list = PluginIndeterminations,PluginAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality
+plugin_list = PluginIndeterminations,PluginSangerAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality
 
 # do not remove cloned sequences
 remove_clonality=false

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 2.0.54
+  version: 2.0.55
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,15 +9,15 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-09-07 00:00:00 Z
+date: 2013-07-24 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
-    - - ">="
+    - &id002 
+      - ">="
       - !ruby/object:Gem::Version 
         version: "0"
   type: :runtime
@@ -26,124 +25,111 @@ dependencies:
 - !ruby/object:Gem::Dependency 
   name: gnuplot
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
     requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    - *id002
   type: :runtime
-  version_requirements: *id002
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: term-ansicolor
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 1.0.5
   type: :runtime
-  version_requirements: *id003
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: xml-simple
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 1.0.12
   type: :runtime
-  version_requirements: *id004
+  version_requirements: *id005
 - !ruby/object:Gem::Dependency 
   name: scbi_blast
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id006 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 0.0.34
   type: :runtime
-  version_requirements: *id005
+  version_requirements: *id006
 - !ruby/object:Gem::Dependency 
   name: scbi_mapreduce
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id007 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 0.0.38
   type: :runtime
-  version_requirements: *id006
+  version_requirements: *id007
 - !ruby/object:Gem::Dependency 
   name: scbi_fasta
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id008 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 0.1.7
   type: :runtime
-  version_requirements: *id007
+  version_requirements: *id008
 - !ruby/object:Gem::Dependency 
   name: scbi_fastq
   prerelease: false
-  requirement: &id008 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id009 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 0.0.17
   type: :runtime
-  version_requirements: *id008
+  version_requirements: *id009
 - !ruby/object:Gem::Dependency 
   name: scbi_plot
   prerelease: false
-  requirement: &id009 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id010 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 0.0.6
   type: :runtime
-  version_requirements: *id009
+  version_requirements: *id010
 - !ruby/object:Gem::Dependency 
   name: scbi_math
   prerelease: false
-  requirement: &id010 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id011 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 0.0.1
   type: :runtime
-  version_requirements: *id010
+  version_requirements: *id011
 - !ruby/object:Gem::Dependency 
   name: scbi_headers
   prerelease: false
-  requirement: &id011 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id012 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 0.0.2
   type: :runtime
-  version_requirements: *id011
+  version_requirements: *id012
 - !ruby/object:Gem::Dependency 
   name: hoe
   prerelease: false
-  requirement: &id012 !ruby/object:Gem::Requirement 
-    none: false
+  requirement: &id013 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         version: 2.8.0
   type: :development
-  version_requirements: *id012
+  version_requirements: *id013
 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
@@ -168,6 +154,7 @@ executables:
 - reverse_paired.rb
 - seqtrimnext
 - split_fastq.rb
+- split_fasta.rb
 - split_ilumina_paired.rb
 - split_paired.rb
 extensions: []
@@ -183,7 +170,7 @@ extra_rdoc_files:
 - lib/seqtrimnext/templates/genomics_short_reads_2.txt
 - lib/seqtrimnext/templates/transcriptomics_454.txt
 - lib/seqtrimnext/templates/transcriptomics_short_reads.txt
-- lib/seqtrimnext/templates/transcriptomics_plants.txt
+- lib/seqtrimnext/templates/transcriptomics_454_plants.txt
 - Manifest.txt
 - PostInstall.txt
 files: 
@@ -207,12 +194,15 @@ files:
 - bin/reverse_paired.rb
 - bin/seqtrimnext
 - bin/split_fastq.rb
+- bin/split_fasta.rb
 - bin/split_ilumina_paired.rb
 - bin/split_paired.rb
 - History.txt
 - 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_sanger_left_adapter.rb
+- lib/seqtrimnext/actions/action_sanger_right_adapter.rb
 - lib/seqtrimnext/actions/action_user_contaminant.rb
 - lib/seqtrimnext/actions/action_empty_insert.rb
 - lib/seqtrimnext/actions/action_ignore_repeated.rb
@@ -263,6 +253,7 @@ files:
 - lib/seqtrimnext/classes/sequence_with_action.rb
 - lib/seqtrimnext/plugins/plugin.rb
 - lib/seqtrimnext/plugins/plugin_ab_adapters.rb
+- lib/seqtrimnext/plugins/plugin_sanger_adapters.rb
 - lib/seqtrimnext/plugins/plugin_adapters.rb
 - lib/seqtrimnext/plugins/plugin_amplicons.rb
 - lib/seqtrimnext/plugins/plugin_contaminants.rb
@@ -288,7 +279,7 @@ files:
 - lib/seqtrimnext/templates/genomics_short_reads_2.txt
 - lib/seqtrimnext/templates/transcriptomics_454.txt
 - lib/seqtrimnext/templates/transcriptomics_short_reads.txt
-- lib/seqtrimnext/templates/transcriptomics_plants.txt
+- lib/seqtrimnext/templates/transcriptomics_454_plants.txt
 - lib/seqtrimnext/utils/extract_samples.rb
 - lib/seqtrimnext/utils/fasta2xml.rb
 - lib/seqtrimnext/utils/global_match.rb
@@ -311,6 +302,8 @@ files:
 homepage: http://www.scbi.uma.es/downloads
 licenses: []
 
+metadata: {}
+
 post_install_message: PostInstall.txt
 rdoc_options: 
 - --main
@@ -318,23 +311,17 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  - *id002
 required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  - *id002
 requirements: []
 
 rubyforge_project: seqtrimnext
-rubygems_version: 1.8.24
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data
 test_files: 
 - test/test_helper.rb