seqtrimnext 2.0.51 → 2.0.52

data/lib/seqtrimnext/plugins/plugin_rem_adit_artifacts.rb

@@ -1,245 +0,0 @@
-require "plugin"
-
-
-########################################################
-# Author: Almudena Bocinos Rioboo                      
-# 
-# Defines the main methods that are necessary to execute PluginRemAditArtifacts
-
-#                                                     
-# Inherit: Plugin
-########################################################
-
-class PluginRemAditArtifacts < Plugin
-  
-  
-  
- # Begins the plugin_low_high_size's execution whit the sequence "seq"
- # Returns a list with start of polyA or polyT seq or 0 if not found
- #     start of a possible second polyAT what was found in the second search, since it looks for both
- # Uses the param polyA_length to look for at least that number of contiguous A's
- def execute(seqs)
-   seqs.each do |s|
-       exec_seq(s)
-    end
-  end
-
-
-  def exec_seq(seq)
-   
-    $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: removing artifacts into the sequence"    
-    seq2 = seq.seq_fasta    
-    first = 0
-    last = seq2.size-1    
-    old_first=first
-    old_last=last
-      
-
-    while (seq2 =~ /^(GCGGGG|CCCCGC)/i)
-      first += 6
-      seq2.slice!(0..5)
-    end
-    
-    
-    while (seq2 =~ /(GCGGGG|CCCCGC)$/i)
-      last -= 6
-      seq2.slice!(seq2.size-1-5..seq2.size-1)
-      
-    end
-   
-    
-    #is_forward, is_cDNA, 
-    #TrimExtremeNXs(first,last)
-    is_forward = @params.get_param('is_forward')=='true'
-    is_cDNA = @params.get_param('is_cDNA')=='true'
-     
-    previous_first,previous_last =0,0
-    
-    until ((previous_first == first) && (previous_last == last))
-      previous_first,previous_last = first, last      
-    
-      if (is_cDNA)
-        if (is_forward)
-           
-          nTs = 0
-          nTs = $1.length if (seq2 =~ /^(T+)/i) 
-          
-          if (nTs > 3)
-            seq2.slice!(0..nTs -1)            
-            first += nTs #-1
-           
-          end
-          
-          nAs = 0
-          nAs = $1.length if (seq2 =~ /(A+)$/i)
-        
-          if (nAs > 3)            
-            seq2.slice!(seq2.size - nAs..seq2.size - 1)
-            last -= nAs
-            
-          end
-        else #si es backward
-           
-          nTs = 0
-          nTs = $1.length if (seq2 =~ /(T+)$/i) 
-          
-          if (nTs > 3)            
-            seq2.slice!(seq2.size-nTs..seq2.size-1)
-            last -= nTs
-            
-          end
-    
-          nAs = 0
-          nAs = $1.length if (seq2 =~ /^(A+)/i)
-          
-          if (nAs > 3)            
-            seq2.slice!(0..nAs -1)
-            first += nAs
-          
-          end
-        end    
-      end
-    end 
-    
-      
-    if (((first>=0) && (first>old_first)) || ((last>=0) && (last<old_last)))
-      type='ActionRemAditArtifacts'           
-      actions = []          
-      # seq.add_action(first,last,type)  
-      a=seq.new_action(first,last,type) 
-      actions.push a
-      seq.add_actions(actions)    
-    end
-   
-    
-  end
-  ######################################################################
-  #---------------------------------------------------------------------
-  def execute_old(seq)
-    seq2 = seq.seq_fasta   
-    #seq2 = 'dGCGGGG' 
-    first = 0
-    last = seq2.size-1    
-    old_first=first
-    old_last=last
-      
-    # puts '1 '+seq2
-    # puts 'POS '+first.to_s
-    # puts 'POS '+last.to_s
-    while (seq2 =~ /^(GCGGGG|CCCCGC)/i)
-      first += 6
-      seq2.slice!(0..5)
-     # puts '2 '+seq2
-     # already = true
-    end
-    
-    
-    while (seq2 =~ /(GCGGGG|CCCCGC)$/i)
-      last -= 6
-      seq2.slice!(seq2.size-1-5..seq2.size-1)
-      # puts '3 '+seq2
-     # already = true
-    end
-   
-    
-    #is_forward, is_cDNA, 
-    #TrimExtremeNXs(first,last)
-    is_forward = @params.get_param('is_forward')
-    is_cDNA = @params.get_param('is_cDNA')
-     # puts '4 '+seq2
-     previous_first,previous_last =0,0
-    
-    until ((previous_first == first) && (previous_last == last))
-      previous_first,previous_last = first, last
-      # puts 'POS5-F '+first.to_s
-      # puts 'POS5-L '+last.to_s
-    
-      if (is_cDNA)
-        if (is_forward)
-           # puts '5 '+seq2
-          nTs = 0
-          nTs = $1.length if (seq2 =~ /^(T+)/i) 
-          if (nTs > 3)
-            seq2.slice!(0..nTs -1)
-             # puts '6 '+seq2
-            first += nTs #-1
-            # puts 'POS6-F '+first.to_s
-          end
-          nAs = 0
-          nAs = $1.length if (seq2 =~ /(A+)$/i)
-          # puts '6-7 '+seq2 + nAs.to_s
-          if (nAs > 3)
-            # puts '7 '+seq2
-            seq2.slice!(seq2.size - nAs..seq2.size - 1)
-            last -= nAs#seq2.size-nAs-2
-            # puts 'POS7-L '+last.to_s
-          end
-        else #si es backward
-           # puts '5b '+seq2
-          nTs = 0
-          nTs = $1.length if (seq2 =~ /(T+)$/i) 
-          if (nTs > 3)
-             # puts '6b '+seq2
-            seq2.slice!(seq2.size-nTs..seq2.size-1)
-            last -= nTs#seq2.size-nTs -2
-            # puts 'POS6b-L '+last.to_s
-          end
-    
-          nAs = 0
-          nAs = $1.length if (seq2 =~ /^(A+)/i) 
-          if (nAs > 3)
-             # puts '7b '+seq2
-            seq2.slice!(0..nAs -1)
-            first += nAs#nAs -1
-            # puts 'POS7b-f '+first.to_s
-          end
-        end    
-      end
-    end 
-    
-       #first -= 1 if (old_first!= first) 
-        #last += 1 if (old_last!= last)
-    
-    # puts 'POS7-8 '+first.to_s
-    # puts 'POS7-8 '+last.to_s
-      
-    if (((first>=0) && (first>old_first)) || ((last>=0) && (last<old_last)))
-      type='ActionRemAditArtifacts'
-            
-       # puts '8 '+seq2
-      seq.add_action(first,last,type)    
-    end
-     # puts '9 '+seq2
-    
-  end
-  
- 
-
-  ######################################################################
-  #---------------------------------------------------------------------
-
-  #Returns an array with the errors due to parameters are missing 
-  def self.check_params(params)
-    errors=[]
-    
-    
-    
-#    if !params.exists?('ta')
-#      errors.push " The param <ta> doesn't exist"
-#    end
-    
-#    if !params.exists?('poly_at_length')
-#      errors.push " The param <poly_at_length> doesn't exist"
-#    end
-    
-
-    
-    return errors
-  end
-  
-  
-  
-  
-  
-  
-end