Class: PluginUserContaminants

Inherits:
Plugin
  • Object
show all
Defined in:
lib/seqtrimnext/plugins/plugin_user_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, 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_user_contaminants.rb', line 141

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_user_contaminant','Float',default_value,comment)

  comment='Minimum required identity (%) for a reliable user contaminant match'
  default_value = 85
  params.check_param(errors,'blast_percent_user_contaminant','Integer',default_value,comment)

  comment='Minimum hit size (nt) for considering for user contaminant'
  default_value = 30 # era 40
  params.check_param(errors,'min_user_contaminant_size','Integer',default_value,comment)

  comment='Path for user contaminant database'
  default_value = "" #File.join($FORMATTED_DB_PATH,'user_contaminant.fasta')
  params.check_param(errors,'user_contaminant_db','DB',default_value,comment)

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

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

  return errors
end

Instance Method Details

#can_execute? ⇒ Boolean

Returns:

  • (Boolean) 


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

def can_execute?
  return !@params.get_param('user_contaminant_db').empty?
end

#do_blasts(seqs) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_user_contaminants.rb', line 41

def do_blasts(seqs)

  # 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_user_contaminants')
  extra_params=@params.get_param('blast_extra_params_user_contaminants')

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

  blast = BatchBlast.new("-db #{@params.get_param('user_contaminant_db')}",'blastn'," -task #{task_template} #{extra_params} -evalue #{@params.get_param('blast_evalue_user_contaminant')} -perc_identity #{@params.get_param('blast_percent_user_contaminant')} -culling_limit 1")  #get classify -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


  #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)


  return blast_table_results
end

#exec_seq(seq, blast_query) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_user_contaminants.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.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for classify into the sequence"

  type = "ActionUserContaminant"

  classify={}
  contaminants=[]

  
  merge_hits(blast_query.hits,contaminants,nil,false)

  begin
    contaminants2=contaminants
    contaminants = []                            #second round to save contaminants without overlap
    merge_hits(contaminants2,contaminants,nil,false)
  end until (contaminants2.count == contaminants.count)
  
  contaminants.sort {|c1,c2| (c1.q_end - c1.q_beg + 1)<=>(c2.q_end - c2.q_beg + 1)}

  # classify=sum_hits_by_id(contaminants.hits)

  actions=[]
  # classify_size=0

  min_cont_size=@params.get_param('min_user_contaminant_size').to_i
  
  # biggest_classify = contaminants.sort {|c1,c2| c1[1]<=>c2[1]}
  
  if !contaminants.empty?

    # definition,classify_size = biggest_classify.last
    
    biggest_contaminant=contaminants.last
    hit_size=(biggest_contaminant.q_end - biggest_contaminant.q_beg + 1)
    
    a = seq.new_action(biggest_contaminant.q_beg,biggest_contaminant.q_end,type) # adds the correspondent action to the sequence

    a.message = biggest_contaminant.definition
    
    seq.add_comment("Contaminated: #{biggest_contaminant.definition}")
    
    a.tag_id = biggest_contaminant.definition.gsub(' ','_')

    # a.found_definition = c.definition    # save the classify definitions, each separately
    
    #save to this file
    seq.add_file_tag(0, 'with_user_contaminant', :both, 10)
    
    actions.push a
    
    add_stats('user_contaminant_size',hit_size)
    add_stats('user_contaminant_ids',biggest_contaminant.definition)

    seq.add_actions(actions)
  end

end

#near_to_extrem(c, seq, min_cont_size) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_user_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

#sum_hits_by_id(hits) ⇒ Object 



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

def sum_hits_by_id(hits)
  res={}
  
  hits.each do |c|
    hit_size=c.q_end - c.q_beg + 1
    
    res[c.definition] = (res[c.definition]||0)+hit_size
    
  end
  
  puts res.to_json
  return res
end