Class: PluginAdapters

Inherits:
Plugin
  • Object
show all
Defined in:
lib/seqtrimnext/plugins/plugin_adapters.rb

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginAdapters

Inherit: Plugin

Instance Attribute Summary

Attributes inherited from Plugin

#stats

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Plugin

#add_stats, #add_text_stats, auto_setup, check_param, get_graph_filename, get_graph_title, graph_ignored?, ignored_graphs, #initialize, #merge_hits, #overlapX?, plot_setup, valid_graphs

Constructor Details

This class inherits a constructor from Plugin

Class Method Details

.check_params(params) ⇒ Object

Returns an array with the errors due to parameters are missing



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# File 'lib/seqtrimnext/plugins/plugin_adapters.rb', line 146

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

Instance Method Details

#cut_by_right(adapter, seq) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_adapters.rb', line 36

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

#do_blasts(seqs) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_adapters.rb', line 56

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.info('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

#exec_seq(seq, blast_query) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_adapters.rb', line 78

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.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 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

#execute(seqs) ⇒ Object

Begins the plugin1’s execution to warn that there are contaminants in the sequence “seq”



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# File 'lib/seqtrimnext/plugins/plugin_adapters.rb', line 48

def execute(seqs)
  blasts= do_blasts(seqs)
  
  seqs.each_with_index do |s,i|
    exec_seq(s,blasts.querys[i])
  end
end

#get_type_adapter(p_start, p_end, seq) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_adapters.rb', line 12

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