Class: PluginContaminants

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

Constant Summary collapse

MAX_TARGETS_SEQS =

MAXIMUM NUMBER OF DIFFERENT ALIGNED SEQUENCES TO KEEP FROM BLAST DATABASE

4

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_contaminants.rb', line 195

def self.check_params(params)
  errors=[]


  comment='Blast E-value used as cut-off when searching for contaminations'
  default_value = 1e-10
  params.check_param(errors,'blast_evalue_contaminants','Float',default_value,comment)

  comment='Minimum required identity (%) for a reliable contamination'
  default_value = 85
  params.check_param(errors,'blast_percent_contaminants','Integer',default_value,comment)

  comment='Minimum hit size (nt) for considering a true contamination'
  default_value = 40
  params.check_param(errors,'min_contam_seq_presence','Integer',default_value,comment)

  comment='Genus of input data: contaminations belonging to this genus will be ignored'
  default_value = ''
  params.check_param(errors,'genus','String',default_value,comment)

  comment='Is a contamination considered a source of sequence rejection? (setting to false will only trim contaminated sequences instead of rejecting the complete read)'
  default_value = 'true'
  params.check_param(errors,'contaminants_reject','String',default_value,comment)

  comment='Path for contaminants database'
  default_value = File.join($FORMATTED_DB_PATH,'contaminants.fasta')
  params.check_param(errors,'contaminants_db','DB',default_value,comment)

  comment='Blast task template for contaminations'
  #default_value = 'blastn'
  default_value = 'megablast'
  params.check_param(errors,'blast_task_template_contaminants','String',default_value,comment)

  comment='Blast extra params for contaminations'
  #default_value = ''
  default_value = '"-word_size=22"'
  params.check_param(errors,'blast_extra_params_contaminants','String',default_value,comment)

  return errors
end

Instance Method Details

#do_blasts(seqs) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_contaminants.rb', line 22

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

  # This message is due to short sequences
  #Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options 

  # TODO - Culling limit = 2 porque el blast falla con este comando cuando se le pasa cl=1 y dust=no
  # y una secuencia de baja complejidad como entrada

  task_template=@params.get_param('blast_task_template_contaminants')
  extra_params=@params.get_param('blast_extra_params_contaminants')

  extra_params=extra_params.gsub(/^\"|\"?$/, '')

  #blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task blastn  -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}

  blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task #{task_template} #{extra_params} -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}

  $LOG.debug('BLAST:'+blast.get_blast_cmd(:table))

  fastas=[]

  seqs.each do |seq|
    fastas.push ">"+seq.seq_name
    fastas.push seq.seq_fasta
  end

  # fastas=fastas.join("\n")
  # $LOG.info('doing blast to:')
  # $LOG.info('-'*20)
  # $LOG.info(fastas)
  # $LOG.info('-'*20)

  #blast_table_results = blast.do_blast(fastas,:xml)
  t1=Time.now
  #blast_table_results = blast.do_blast(fastas,:xml,false)
  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)

  # $LOG.info(blast_table_results.inspect)

  return blast_table_results
end

#exec_seq(seq, blast_query) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_contaminants.rb', line 76

def exec_seq(seq,blast_query)
  
  user_conts=seq.get_actions(ActionUserContaminant)
  
  if (!user_conts.nil?) && (!user_conts.empty?)
    return
  end
  
  #if blast_query.query_def != seq.seq_name
  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 contaminants into the sequence"

  #add_plugin_stats('hsp_count',seq.seq_name,blast_query.hits.count) 

  #blast = BatchBlast.new('-db DB/formatted/contaminants.fasta','blastn',' -task blastn -evalue 1e-10 -perc_identity 95')  #get contaminants
  # blast = BatchBlast.new("-db #{@params.get_param('contaminants_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_contaminants')} -perc_identity #{@params.get_param('blast_percent_contaminants')} -culling_limit 1")  #get contaminants -max_target_seqs #{MAX_TARGETS_SEQS}


  # blast_table_results = blast.do_blast(seq.seq_fasta,:xml)             #rise seq to contaminants  executing over blast


  #blast_table_results = BlastTableResult.new(res)

  type = "ActionIsContaminated"

  contaminants=[]

  contaminants_ids=[]

  # blast_table_results.querys.each do |query|     #first round to save contaminants without overlap
  # contaminants_ids.push query.hits.definition if (not contaminants_ids.include?(query.hits.definition))
  merge_hits(blast_query.hits,contaminants,contaminants_ids)
  # end




  begin
    contaminants2=contaminants
    contaminants = []                            #second round to save contaminants without overlap
    merge_hits(contaminants2,contaminants)
    #  DONE describir cada ID contaminante encontradomerge_hits(contaminants2,contaminants,ids_contaminants)
  end until (contaminants2.count == contaminants.count)


  actions=[]
  contaminants_size=0

  # @stats[:contaminants_size]={}
  # @stats['contaminants_size']={}
  # @stats['rejected_seqs']={}

  min_cont_size=@params.get_param('min_contam_seq_presence').to_i

  contaminants.each do |c|
    contaminants_size=c.q_end - c.q_beg + 1
    #if ( (@params.get_param('genus')!=c.subject_id.split('_')[1]) &&
    valid_genus=@params.get_param('genus').empty? || !c.definition.upcase.index(@params.get_param('genus').upcase)

    if (valid_genus) &&
        (contaminants_size>=min_cont_size)

      #( (min_cont_size<=contaminants_size) || (near_to_extrem(c,seq,min_cont_size)) ) )

      if !seq.range_inside_action_type?(c.q_beg,c.q_end,ActionVectors)

        # puts "DIFFERENT SPECIE #{specie} ,#{hit.subject_id.split('_')[1].to_s}"
        a = seq.new_action(c.q_beg,c.q_end,type) # adds the correspondent action to the sequence
        a.message = c.definition

        a.found_definition = contaminants_ids    # save the contaminants definitions, each separately
        actions.push a

        contaminants_size=c.q_end-c.q_beg+1

        # if @stats[:contaminants_size][contaminants_size].nil?
        #           @stats[:contaminants_size][contaminants_size] = 0
        #        end
        #
        #        @stats[:contaminants_size][contaminants_size] += 1
        add_stats('contaminants_size',contaminants_size)
        contaminants_ids.each do |c|
          add_stats('contaminants_ids',c)
        end

      end
    else
      $LOG.debug('Contaminant ignored due to genus match: '+c.definition)
    end
  end

  reject=@params.get_param('contaminants_reject')
  # cond_if=false
  #   cond_if=true if (not actions.empty? ) && (reject=='true')
  #
  #   puts "Before check SEQ_REJECTED= TRUE  (reject= .#{reject}. #{reject.class}&& not actions empty= #{not actions.empty?} ) == #{cond_if} >>> "



  if ((not actions.empty? ) && (reject.to_s=='true'))
    #reject sequence
    # puts "SEQ_REJECTED= TRUE >>> "
    seq.seq_rejected=true
    seq.seq_rejected_by_message='contaminated'

    # @stats[:rejected_seqs]={'rejected_seqs_by_contaminants' => 1}
    add_stats('rejected','contaminated')

  end

  seq.add_actions(actions)


end

#near_to_extrem(c, seq, min_cont_size) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_contaminants.rb', line 17

def near_to_extrem(c,seq,min_cont_size)
  max_to_extreme=(min_cont_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