Class: PluginMids

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

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginMids

Inherit: Plugin

Constant Summary collapse

SIZE_SEARCH_MID = 
20
MAX_MID_ERRORS = 
2

Instance Attribute Summary

Attributes inherited from Plugin

#stats

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Plugin

#add_plugin_stats, #add_stats, #add_text_stats, auto_setup, #can_execute?, check_param, #execute, 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_mids.rb', line 201

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

comment='Minimum required identity (%) for a reliable MID'
default_value = 95
params.check_param(errors,'blast_percent_mids','Integer',default_value,comment)
  
  comment='Path for MID database'
default_value = File.join($FORMATTED_DB_PATH,'mids.fasta')
params.check_param(errors,'mids_db','DB',default_value,comment)

  return errors
end

Instance Method Details

#do_blasts(seqs) ⇒ Object

MIN_MID_SIZE = 7 # very important, don’t touch DB_MID_SIZE = 10 # DONE read formatted db and save the mid sizes



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# File 'lib/seqtrimnext/plugins/plugin_mids.rb', line 18

def do_blasts(seqs)
   # find MIDS  with less results than max_target_seqs value 
   blast = BatchBlast.new("-db #{@params.get_param('mids_db')}",'blastn'," -task blastn-short    -perc_identity #{@params.get_param('blast_percent_mids')} -max_target_seqs 4 ")  #get mids 
   $LOG.debug('BLAST:'+blast.get_blast_cmd)

   fastas=[]
   
   seqs.each do |seq|
    fastas.push ">"+seq.seq_name
    fastas.push seq.seq_fasta[0..SIZE_SEARCH_MID]
   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_mids.rb', line 40

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 mids into the sequence"   
    

   # blast_table_results = blast.do_blast(seq.seq_fasta[0..SIZE_SEARCH_MID])             # execute blast to find mids
   # blast_table_results.inspect
   
   actions=[]
   file_tag='no_MID'
   
   key_size=0
   mid_size=0
   
   key_already_found=!seq.get_actions(ActionKey).empty?
   
   mid_errors=[]    #number of MIDs with 1 error, and number of MIDs with 2 errors
   mid_id=[] #number of MIDs from each type
   mid_found = false
   
   if !blast_query.hits.empty? # mid found 
     
     # blast_query.hits.sort!{|h1,h2| h1.q_beg <=> h2.q_beg}
     # puts blast_query.count.to_s + "============== #{blast_query.hits[0].inspect}"
     # blast_table_results.inspect
                                
     # select first sorted mid
     mid=blast_query.hits[0]
     
     # find a not reversed mid
     if mid.reversed
       
       blast_query.hits.each do |hit|
        if !hit.reversed # take the first non-reversed one
           mid = hit
           break
        end
       end

     end
     
     # puts "DOES THE MID HAVE ENOUGHT SIZE? #{mid.q_end-mid.q_beg+1} >= #{MIN_MID_SIZE}?"
     mid_size=mid.q_end-mid.q_beg+1
     
     db_mid=@params.get_mid(mid.subject_id)
     db_mid_size = db_mid.size  #get mid's size from DB   
     
     mid_initial_pos=mid.q_beg-mid.s_beg
     has_full_key=false
     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
     
     if mid.reversed
     	  # discard mid
     elsif (mid.gaps+mid.mismatches > MAX_MID_ERRORS) # number of ERRORS and GAPs is higher than MAX_MID_ERRORS, 
        # discard mid
     elsif (mid.q_beg<3) # if found mid starts below 3, then discard it 
       # discard mid
     elsif (has_full_key && (mid_initial_pos >=6))
       # discard mid
     elsif (!has_full_key && (mid_initial_pos >=7))
       # discard mid
     elsif (mid_size >= db_mid_size-1)  # MID found and MID's size is enought, THEN create key and mid
		 		 
       key_beg,key_end=[0,mid.q_beg-1]
       key_size=mid.q_beg
      
       # Create an ActionKey before the ActionMid
       if key_size>0 && !key_already_found                                    
         a = seq.new_action(key_beg,key_end,"ActionKey") # adds the actionKey to the sequence
         actions.push a 
       end      
       
				 #Create an ActionMid 
         a = seq.new_action(mid.q_beg,mid.q_end,"ActionMid") # adds the ActionMids to the sequence   
         a.message = mid.subject_id
         a.tag_id = mid.subject_id
         file_tag = mid.subject_id
         actions.push a
       
         mid_found = true
       
    elsif (mid_size >= db_mid_size-3)
      # To recover a MID it must start or end in one edge
      if (mid.s_beg==0) || (mid.s_end==mid_size)

			new_q_beg, new_q_end, recovered_size,recovered_mid = recover_mid(mid, db_mid, seq.seq_fasta[0..SIZE_SEARCH_MID])
			
			$LOG.debug("Recover mid: #{recovered_mid} valid (#{recovered_size} >= #{10-1}) = #{recovered_size>=10-1}, #{seq.seq_fasta[new_q_beg..new_q_end]}")

			if recovered_size >= db_mid_size-1
				mid_size = recovered_size
		
				# if MID found and MID's size is enought to recover a MID, THEN create an action key and mid 
				key_beg,key_end=[0,new_q_beg-1]
				key_size=new_q_beg
			
				$LOG.debug "RECOVER OUTPUT: #{new_q_beg} #{new_q_end} #{recovered_size}"

				#  if key_size > 4(or max_size_key) then seq.seq_rejected 

				# Create an ActionKey before the ActionMid
				if key_size>0 && !key_already_found
					a = seq.new_action(key_beg,key_end,"ActionKey") # adds the actionKey to the sequence
					actions.push a 
				end      

				#Create an ActionMid to a recovered mid
				a = seq.new_action(new_q_beg,new_q_end,"ActionMid") # adds the ActionMids to the sequence 
				a.message = "Recovered " + mid.subject_id
				a.tag_id = mid.subject_id
          file_tag = mid.subject_id
				actions.push a
				add_stats('recovered_mid_id',mid.subject_id)

				mid_found = true
	    end
    end
  end
  end
   
  if !mid_found && !key_already_found # MID not found, take only the key
     mid_size=0
     key_beg,key_end=[0,3]
     key_size=4
     a = seq.new_action(key_beg,key_end,'ActionKey') # adds the actionKey to the sequence
     actions.push a   
   end 
   
   #Add actions  
   seq.add_actions(actions)
   
   seq.add_file_tag(1, file_tag, :both)
   # seq.add_file_tag(2,'sequence')
   
   if (mid_found) # MID without errors
    
     add_stats('mid_id',mid.subject_id)
     add_stats('mid_id','total')

     #save MID count by ID
     add_stats(mid.subject_id,mid_size)
    
    	if (mid.gaps+mid.mismatches > 0)
		add_stats('mid_with_errors',mid.gaps+mid.mismatches)
    	end
     
   end
   
   if !key_already_found
     add_stats('key_size',key_size)
     add_stats('mid_size',mid_size)
   end
end