Class: PluginAmplicons

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

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginAdapters Inherit: Plugin

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_amplicons.rb', line 147

def self.check_params(params)
  errors=[]

  comment='Blast E-value used as cut-off when searching for primers'
  # default_value = 1e-6
  default_value = 1
  params.check_param(errors,'blast_evalue_primers','Float',default_value,comment)

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

  comment='Minimun primer size'
  default_value = 15
  params.check_param(errors,'min_primer_size','Integer',default_value,comment)

  comment='Path for primers database'
  # default_value = File.join($FORMATTED_DB_PATH,'adapters_ab.fasta')
  default_value=nil
  params.check_param(errors,'primers_db','DB',default_value,comment)

  return errors
end

Instance Method Details

#do_blasts(seqs) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_amplicons.rb', line 25

def do_blasts(seqs)
  # find MIDS  with less results than max_target_seqs value
  blast=BatchBlast.new("-db #{@params.get_param('primers_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_primers')}")
  $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)

  # 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_amplicons.rb', line 47

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 primers into the sequence"

  # puts blast_query.inspect
  
  # merge hits
  # primers=blast_query.merged_hits!
  
  # do not merge hits, since id is important
  primers=blast_query.hits
  
  min_primer_size=@params.get_param('min_primer_size').to_i
  # puts "MERGED:"
  # puts primers.inspect

  # type = 'ActionAbAdapter'
  actions=[]
  adapter_size=0

  # filter primers by size
  primers = primers.select{|primer| (primer.size >= min_primer_size)}.sort{|p1,p2| p1.size<=>p2.size}.reverse
  # puts "FILTERED:"
  # puts primers.inspect
  
  # reject sequences with less than two primers
  if primers.count < 2

    seq.seq_rejected=true
    seq.seq_rejected_by_message='Primer pair not found'

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

  else # has two primers, or more

    if seq.seq_fasta.index('N')
      seq.seq_rejected=true
      seq.seq_rejected_by_message='At least one N found'

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

    else
      # puts "EL DE ARRIBA"
      
      # take first two primers and order them by qbeg
      left_primer = primers[0..1].sort{|p1,p2| p1.q_beg<=>p2.q_beg}.first
      right_primer = primers[0..1].sort{|p1,p2| p1.q_beg<=>p2.q_beg}.last
      
      # puts "LEFT_PRIMER:"
      # puts left_primer.inspect
      # puts "RIGHT_PRIMER:"
      # puts right_primer.inspect

      # if (left_primer.size>= min_primer_size) && (right_primer.size>= min_primer_size)

        a = seq.new_action(left_primer.q_beg,left_primer.q_end,'ActionLeftPrimer')
        a.message = left_primer.subject_id
        a.tag_id = left_primer.subject_id
        a.reversed = left_primer.reversed
        a.left_action = true
        actions.push a

        add_stats('primer_size',left_primer.size)
        add_stats('primer_id',left_primer.subject_id)

        a = seq.new_action(right_primer.q_beg,right_primer.q_end,'ActionRightPrimer')
        a.message = right_primer.subject_id
        a.reversed = right_primer.reversed
        a.tag_id = right_primer.subject_id
        a.right_action = true
        actions.push a

        add_stats('primer_size',right_primer.size)
        add_stats('primer_id',right_primer.subject_id)
        
        seq.add_file_tag(2, left_primer.subject_id, :file)
        seq.add_file_tag(2, right_primer.subject_id, :file)
        

      # end


      if !actions.empty?
        seq.add_actions(actions)
        add_stats('sequences_with_primers','count')
        
        # add_stats('sequences',seq.seq_fasta)
      end

    end
    #
  end
end

#execute(seqs) ⇒ Object

adapters found at end of sequence are even 2 nt wide, cut in 5 because of statistics MIN_PRIMER_SIZE = 5 MIN_FAR_ADAPTER_SIZE = 13 MIN_LEFT_ADAPTER_SIZE = 9 Begins the plugin1’s execution to warn that there are contaminants in the sequence “seq”



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

def execute(seqs)
  blasts= do_blasts(seqs)

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