Class: PluginLinker

Inherits:
Plugin show all
Defined in:
lib/seqtrimnext/plugins/plugin_linker.rb

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginLinker

Inherit: Plugin

Constant Summary collapse

MAX_LINKER_ERRORS = 
2

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_linker.rb', line 216

def self.check_params(params)
  errors=[]  
  
  comment='Blast E-value used as cut-off when searching for linkers in paired-ends'
default_value = 1e-10
params.check_param(errors,'blast_evalue_linkers','Float',default_value,comment)

comment='Minimum required identity (%) for a reliable linker'
default_value = 95
params.check_param(errors,'blast_percent_linkers','Integer',default_value,comment)

  
  return errors
end

Instance Method Details

#do_blasts(seqs) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 82

def do_blasts(seqs)
   # find MIDS  with less results than max_target_seqs value 
   blast = BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'linkers.fasta')}",'blastn'," -task blastn-short  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers          

   $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_linker.rb', line 105

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 linker into the sequence"
   
   # key_beg,key_end=search_key(seq,0,3)   if false       
   # blast = BatchBlast.new("-subject #{File.join($FORMATTED_DB_PATH,'linkers.fasta')}",'blastn'," -task blastn  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers
   # blast = BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'linkers.fasta')}",'blastn'," -task blastn-short  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers          
   # 
   # blast_table_results = blast.do_blast(seq.seq_fasta)             #rise seq to linkers  executing over blast 
  

   #blast_table_results = BlastTableResult.new(res) 
   actions=[]  
   linker_size=0
        
   if (!blast_query.hits.empty?) #linker found
   
  linkers = merge_hits_with_same_qbeg_and_qend(blast_query.hits)

  if linkers.count ==1
  
       linker=linkers.first
       
       linker_size=linker.q_end-linker.q_beg+1
     
     if (linker.gaps+linker.mismatches>MAX_LINKER_ERRORS) # number of ERRORS and GAPs is higher than MAX_LINKER_ERRORS, 
         seq.seq_rejected=true
         seq.seq_rejected_by_message='linker with mismatches'
         # @stats[:rejected_seqs]={'rejected_seqs_by_errors' => 1}
         add_stats('rejected','by_linker_errors')
          add_stats('linker_errors',linker.gaps+linker.mismatches)
     else     
       #Create an ActionLinker
        a = seq.new_action(linker.q_beg,linker.q_end,'ActionLinker') # adds the ActionLinker to the sequence 
        a.message = linker.subject_id 
        a.tag_id = linker.subject_id
        actions.push a  
        
          # seq.add_file_tag(0, 'paired', :file)
        
        add_stats('linker_id',linker.subject_id)
        add_stats('linker_id','total')
        
     end
     
  else # multiple linkers found
    q_begs=[]
    q_ends=[]

    linker_count=linkers.count
    
    linkers.each do |linker|
      #puts "*MULTILINKER* #{linker.subject_id[0..40].ljust(40)} #{linker.q_beg.to_s.rjust(6)} #{linker.q_end.to_s.rjust(6)} #{linker.s_beg.to_s.rjust(6)} #{linker.s_end.to_s.rjust(6)}"
      q_begs.push linker.q_beg
      q_ends.push linker.q_end

    end
        
      first_linker = linkers.first
      last_linker = linkers.last
      
      a = seq.new_action(q_begs.min,q_ends.max,'ActionMultipleLinker') # adds the ActionLinker to the sequence
      a.message = "#{linker_count} x #{first_linker.subject_id}"
      a.tag_id = first_linker.subject_id
      
      #determine with part (left or right) has the best quality
      left_quals = seq.seq_qual[0,q_begs.min]
    sum_left=sum_quals(left_quals)
      
      right_quals = seq.seq_qual[q_ends.max+1..seq.seq_qual.length]
      sum_right=sum_quals(right_quals)
      
      if sum_left>=sum_right
       a.right_action=true
     else
        a.left_action=true
      end
      
      #puts "SUM QUAL LEFT:#{sum_left} count:#{left_quals.length}"
      #puts "SUM QUAL RIGHT:#{sum_right} count:#{right_quals.length}"
      
      
      actions.push a
      
      add_stats('multiple_linker_id',first_linker.subject_id)
      add_stats('multiple_linker_id','total')
      add_stats('multiple_linker_count',linker_count)
      
#       puts "=== > seq_qual: #{seq.seq_qual.count}"
#        seq.get_qual_inserts.each do |qi|
#           puts "==> #{qi.join(' ')}"
#        end

      end
      
    else # no linker found
    add_stats('without_linker',linker_size)
  end
   
   
  if !actions.empty?
  #Add actions
  seq.add_actions(actions)
 end

end

#execute(seqs) ⇒ Object

Begins the plugin1’s execution to warn that there is linker into the sequence



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# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 74

def execute(seqs)
  blasts= do_blasts(seqs)

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

#merge_hits_with_same_qbeg_and_qend(hits) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 61

def merge_hits_with_same_qbeg_and_qend(hits)
  res =[]

    hits.each do |hit|
    if !res.find{|h| (h.q_beg==hit.q_beg) && (h.q_end==hit.q_end)}
      res.push hit
    end
    end  

    return res
end

#sum_quals(a) ⇒ Object

It’s created an ActionInsert or ActionShortInsert after the ActionLinker

def add_action_after_linker(p_q_end,size_insert,actions,seq)

size_min_insert = @params.get_param('size_min_insert').to_i     

if ((p_q_end<seq.seq_fasta.size-1) && (size_insert>=size_min_insert) )  #if linker's positions are right 
  #It's created an ActionInsert after the ActionLinker
  a = seq.new_action(p_q_end+1,seq.seq_fasta.size-1,"ActionInsert") # adds the ActionInsert to the sequence before adding the actionMid

  actions.push a

elsif (p_q_end<seq.seq_fasta.size-1)   #if linker's positions are right and insert's size is short 
  #It's created an ActionInsert after the ActionLinker
  a = seq.new_action(p_q_end+1,seq.seq_fasta.size-1,"ActionShortInsert") # adds the ActionInsert to the sequence before adding the actionMid

  actions.push a 
end

end



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# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 53

def sum_quals(a)
  res = 0
  
  a.map{|e| res+=e}
  
return res
end