seqtrimnext 2.0.36 → 2.0.38

data/History.txt

@@ -1,3 +1,11 @@
+=== 2.0.38 2011-07-07
+
+Optional Initial Stats generation in templates
+
+=== 2.0.37 2011-07-07
+
+Added option to skip initial stats
+
 === 2.0.36 2011-06-24
 
 Added clustered installation documentation

data/bin/seqtrimnext

@@ -205,6 +205,12 @@ optparse = OptionParser.new do |opts|
   opts.on( '-c', '--check_databases', 'Check Blast databases and reformat if necessary' ) do
     options[:check_db] = true
   end
+  
+  # options[:skip_initial_stats] = false
+  # opts.on( '-k', '--skip_initial_stats', 'Skip initial stats' ) do
+  #   options[:skip_initial_stats] = true
+  # end
+  
 
   options[:install_db] = nil
   opts.on( '-i', '--install_databases TYPE', 'Install base databases and reformat them if necessary') do |db_type|
@@ -234,8 +240,9 @@ optparse = OptionParser.new do |opts|
 
 
   options[:list_db] = nil
-  opts.on( '-L', '--list_db DB_NAME', 'List entries IDs in DB_NAME. Use "-L all" to view all available databases' ) do |value|
-    options[:list_db] = value
+  opts.on( '-L', '--list_db [DB_NAME]', 'List entries IDs in DB_NAME. Use "-L all" to view all available databases' ) do |value|
+    options[:list_db] = true
+    options[:list_db_name] = value
   end
 
   options[:gen_params] = false

data/lib/seqtrimnext/classes/seqtrim.rb

@@ -94,6 +94,9 @@ class Seqtrim
 	  default_value='true'
 	  params.check_param(errors,'remove_clonality','String',default_value,comment)
 
+    comment='Generate initial stats'
+	  default_value='true'
+	  params.check_param(errors,'generate_initial_stats','String',default_value,comment)
 
 		comment='Minimum insert size for every trimmed sequence'
 		default_value = 40
@@ -208,9 +211,14 @@ class Seqtrim
       Dir.mkdir(OUTPUT_PATH)
     end
 
-    $LOG.info "Calculatings stats"
     # Extract global stats
-    ExtractStats.new(sequence_reader,params)
+    if params.get_param('generate_initial_stats')=='true'
+      $LOG.info "Calculatings stats"
+      
+      ExtractStats.new(sequence_reader,params)
+    else
+      $LOG.info "Skipping calculatings stats phase."
+    end
     
     
     # save used params to file

data/lib/seqtrimnext/plugins/plugin_adapters.rb

@@ -107,7 +107,7 @@ class PluginAdapters < Plugin
 
     actions=[] 
     adapter_size=0
-    @stats['adapter_size']={}
+    # @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)

data/lib/seqtrimnext/plugins/plugin_contaminants.rb

@@ -105,8 +105,8 @@ class PluginContaminants < Plugin
     contaminants_size=0
 
     # @stats[:contaminants_size]={}
-    @stats['contaminants_size']={}
-    @stats['rejected_seqs']={}
+    # @stats['contaminants_size']={}
+    # @stats['rejected_seqs']={}
 
     min_cont_size=@params.get_param('min_contam_seq_presence').to_i
 

data/lib/seqtrimnext/plugins/plugin_low_high_size.rb

@@ -28,8 +28,8 @@ class PluginLowHighSize < Plugin
     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)
+    
+    if ((max_size>0 && (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)  

data/lib/seqtrimnext/plugins/plugin_mids.rb

@@ -101,7 +101,7 @@ class PluginMids < Plugin
        
        mid_initial_pos=mid.q_beg-mid.s_beg
        has_full_key=false
-       if @params.get_param('sequencing_key')
+       if !@params.get_param('sequencing_key').nil? && !@params.get_param('sequencing_key').empty?
        	has_full_key = !seq.seq_fasta.index(@params.get_param('sequencing_key')).nil?
        end
        

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 = '2.0.36'
+   VERSION = '2.0.38'
   
   SEQTRIM_VERSION = VERSION
   

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 2.0.36
+  version: 2.0.38
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-06-24 00:00:00 Z
+date: 2011-07-07 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray