Class: PluginVectors

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

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginVectors

Inherit: Plugin

Constant Summary collapse

MAX_TARGETS_SEQS =

MIN_VECTOR_SIZE=30

MAX_TO_EXTREME=(MIN_VECTOR_SIZE/2).to_i

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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_vectors.rb', line 161

def self.check_params(params)
  errors=[] 
  

  comment='Blast E-value used as cut-off when searching for vector fragments'
default_value = 1e-1
params.check_param(errors,'blast_evalue_vectors','Float',default_value,comment)

comment='Minimum required identity (%) for a reliable vector fragment'
default_value = 90
params.check_param(errors,'blast_percent_vectors','Integer',default_value,comment)

  comment='Correct sequences could contain vectors only close to the read end (not within the sequence). The following variable indicates the number of nucleotides from the 5\' or 3\' end that are allowed for considering a vector fragment located at the end. Otherwise, the vector fragment will be qualified as internal and the sequence will be rejected'
default_value = 8
params.check_param(errors,'max_vector_to_end','Integer',default_value,comment)

comment='If a vector fragment is qualified as internal, the fragment should be long enough to be sure that it is a true vector fragment. This is the minimum length of a vector fragment that enables sequence rejection by an internal, unexpected vector'
default_value = 50
params.check_param(errors,'min_vector_seq_presence','Integer',default_value,comment)


  comment='Vectors database path'
default_value = File.join($FORMATTED_DB_PATH,'vectors.fasta')
params.check_param(errors,'vectors_db','DB',default_value,comment)

  comment='Rejects sequences with vectors in the middle'
  default_value = 'true'
  params.check_param(errors,'middle_vector_rejects','String',default_value,comment)


  # params.split_databases('vectors_db')
  
  return errors
end

Instance Method Details

#all_vector_in_linker(vector_beg, vector_end, seq) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_vectors.rb', line 21

def all_vector_in_linker(vector_beg,vector_end,seq)
  linkers=seq.get_actions(ActionLinker) 
  # res=((linkers.count>=1) && (vector_beg>=linkers[0].start_pos) && (vector_end<=linkers[0].end_pos)) 
  # puts " RES #{res}  insert-start #{seq.insert_start} #{linkers.count}>=1 #{vector_beg+seq.insert_start}>=#{linkers[0].start_pos}) && #{vector_end+seq.insert_start}<=#{linkers[0].end_pos})) "
  return  ((linkers.count>=1) && (vector_beg+seq.insert_start>=linkers[0].start_pos) && (vector_end+seq.insert_start<=linkers[0].end_pos))
end

#do_blasts(seqs) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_vectors.rb', line 28

def do_blasts(seqs)
   # find MIDS  with less results than max_target_seqs value 
   blast = BatchBlast.new("-db #{@params.get_param('vectors_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_vectors')} -perc_identity #{@params.get_param('blast_percent_vectors')} -culling_limit 1")  #get vectors

   $LOG.debug('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,:xml)
   
   t1=Time.now
   blast_table_results = blast.do_blast(fastas,:table,false)
   add_plugin_stats('execution_time','blast',Time.now-t1)

   t1=Time.now
   #blast_table_results = BlastStreamxmlResult.new(blast_table_results)
   blast_table_results = BlastTableResult.new(blast_table_results)
   add_plugin_stats('execution_time','parse',Time.now-t1)


   # 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_vectors.rb', line 61

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 vectors into the sequence " 

  #blast contra contaminantes
  
  # blast = BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'vectors.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_vectors')} -perc_identity #{@params.get_param('blast_percent_vectors')} -culling_limit 1")  #get vectors
 
  # blast_table_results = blast.do_blast(seq.seq_fasta,:xml)             #rise seq to contaminants  executing over blast
  type = "ActionVectors"
          
  # puts res
  #     blast_table_results.inspect 
  # blast_table_results.querys.each do |query|     # adds the correspondent action to the sequence
  #      query.hits.each do |hit|
  #        seq.add_action(hit.q_beg,hit.q_end,type)
  #      end
  #    end
  
vectors=[]
vectors_ids=[]
# blast_table_results.querys.each do |query|     # first round to save vectors without overlap     
    # vectors_ids.push query.hits.subject_id if (not vectors_ids.include?(query.hits.subject_id)) 
    merge_hits(blast_query.hits,vectors,vectors_ids)
# end 



begin 
  vectors2=vectors                            # second round to save vectors without overlap
  vectors = []
  merge_hits(vectors2,vectors)
end until (vectors2.count == vectors.count) 

	
actions = [] 
vectors_size=0
min_vector_size=@params.get_param('min_vector_seq_presence').to_i 

vectors.each do |v|                           # adds the correspondent action to the sequence
   
  	 #puts "*VECTOR* #{v.subject_id[0..40].ljust(40)} #{v.q_beg.to_s.rjust(6)} #{v.q_end.to_s.rjust(6)} #{v.s_beg.to_s.rjust(6)} #{v.s_end.to_s.rjust(6)}"

   vector_size=v.q_end-v.q_beg+1  
 # puts " in PLUGIN VECTOR previous to add action #{seq.insert_start} #{seq.insert_end}"   
  # if ((vector_size>=MIN_VECTOR_SIZE) || ((vector_size<MIN_VECTOR_SIZE) && near_to_extrem(v,seq)))
  if (near_to_extrem(v,seq,10) || (vector_size>=min_vector_size)   )
    # puts " near #{near_to_extrem(v,seq,min_vector_size)} #{vector_size}>=#{min_vector_size}"
    #c.q_end+seq.insert_start+max_to_end)>=seq.seq_fasta_orig.size-1)  #if ab adapter is very near to the end of original sequence  
    
    piro_on=@params.get_param('next_generation_sequences').to_s
    
    if (((piro_on=='true')  && (!seq.range_inside_action_type?(v.q_beg,v.q_end,ActionLinker)) && (!seq.range_inside_action_type?(v.q_beg,v.q_end,ActionMultipleLinker)))    ||   # if vectors DB not is contained inside detected linkers
         (piro_on=='false'))

		 # if vector is too big, and it isn't in an extreme, then it is an unexpected vector
       if !near_to_extrem(v,seq,min_vector_size)
     		type = 'ActionUnexpectedVector'

        if @params.get_param('middle_vector_rejects').to_s=='true'
  			  seq.seq_rejected=true
				  seq.seq_rejected_by_message='unexpected vector'
        end
		  
		  add_stats('rejected','unexpected_vector')

     	 end

       
       a = seq.new_action(v.q_beg,v.q_end,type)
       a.message = v.definition  
       # a.found_definition.push  v.subject_id    # save the vectors definitions, each separately    
       a.found_definition=vectors_ids    # save the vectors definitions, each separately   
       a.reversed = v.reversed        
       a.cut=false if (piro_on=='true')  # vectors don't cut when piro is on  
        
       # puts "piro on #{piro_on}  vector cut #{a.cut}  ________________|||||||||| " 
       #          puts " no piro" if (piro_on=='false')    
        
       actions.push a   

       # @stats[:vector_size]={vector_size => 1} 
       add_stats('vector_size',vector_size) 
       vectors_ids.each do |v|
         add_stats('vectors_ids',v)
       end
    end
  end
  
end 

seq.add_actions(actions) 
#
      
end

#near_to_extrem(c, seq, min_vector_size) ⇒ Object

MAXIMUM NUMBER OF DIFFERENT ALIGNED SEQUENCES TO KEEP FROM BLAST DATABASE



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# File 'lib/seqtrimnext/plugins/plugin_vectors.rb', line 16

def near_to_extrem(c,seq,min_vector_size)
  max_to_extreme=(min_vector_size/2).to_i
  return ((c.q_beg-max_to_extreme<0) || (( c.q_end+max_to_extreme)>=seq.seq_fasta.size-1) ) #return if vector is very near to the extremes of insert)
end