Class: PluginAbAdapters

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

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginAdapters

Inherit: Plugin

Constant Summary collapse

MIN_ADAPTER_SIZE =

adapters found at end of sequence are even 2 nt wide, cut in 5 because of statistics

5
MIN_FAR_ADAPTER_SIZE = 
13
MIN_LEFT_ADAPTER_SIZE = 
9

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, graph_ignored?, ignored_graphs, #initialize, #merge_hits, #overlapX?, plot_setup

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_ab_adapters.rb', line 159

def self.check_params(params)
  errors=[]  
  
  comment='Blast E-value used as cut-off when searching for 454 AB adapters'
  # default_value = 1e-6
default_value = 1
params.check_param(errors,'blast_evalue_ab','Float',default_value,comment)

comment='Minimum required identity (%) for a reliable 454 AB adapter'
default_value = 95
params.check_param(errors,'blast_percent_ab','Integer',default_value,comment)

  comment='454 AB adapters can be found only at the read end (not within it). The following variable indicates the number of nucleotides that are allowed for considering the AB adapters to be located at the end'
default_value = 9
params.check_param(errors,'max_ab_to_end','Integer',default_value,comment)
  
  comment='Path for 454 AB adapters database'
default_value = File.join($FORMATTED_DB_PATH,'adapters_ab.fasta')
params.check_param(errors,'adapters_ab_db','DB',default_value,comment)
  
  return errors
end

.get_graph_filename(plugin_name, stats_name) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_ab_adapters.rb', line 191

def self.get_graph_filename(plugin_name,stats_name)
  return stats_name
  
  # case stats_name
  # when 'adapter_type'
  #   'AB adapters by type'
  # when 'adapter_size'
  #   'AB adapters by size'
  # end
end

.get_graph_title(plugin_name, stats_name) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_ab_adapters.rb', line 182

def self.get_graph_title(plugin_name,stats_name)
  case stats_name
  when 'adapter_type'
    'AB adapters by type'
  when 'adapter_size'
    'AB adapters by size'
  end
end

.valid_graphs ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_ab_adapters.rb', line 202

def self.valid_graphs
  return ['adapter_type']
end

Instance Method Details

#do_blasts(seqs) ⇒ Object 



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

def do_blasts(seqs)
   # find MIDS  with less results than max_target_seqs value 
   blast=BatchBlast.new("-db #{@params.get_param('adapters_ab_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_ab')} -word_size #{MIN_ADAPTER_SIZE}")  
   $LOG.info('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_ab_adapters.rb', line 59

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.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for adapters into the sequence" 

      
  # blast=BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'adapters_ab.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_ab')} -perc_identity #{@params.get_param('blast_percent_ab')} -word_size #{MIN_ADAPTER_SIZE}")  
  
  
  
  # blast with only one sequence, no with many sequences from a database
  #---------------------------------------------------------------------
  
  # blast_table_results = blast.do_blast(seq.seq_fasta)             #rise seq to adapterss  executing over blast
  
   #BlastTableResult.new(res)
   # puts blast_query.inspect
   # puts blast_table_results.inspect
   
   filter_hits(blast_query.hits, seq.seq_fasta.length)
  
  adapters=[]
  # blast_table_results.querys.each do |query|     # first round to save adapters without overlap
    merge_hits(blast_query.hits,adapters)
  # end

  begin 
    adapters2=adapters                            # second round to save adapters without overlap
    adapters = []
    merge_hits(adapters2,adapters)
  end until (adapters2.count == adapters.count)

  # puts "MERGED"
  # puts "="*50
  # adapters.each {|a| puts a.inspect}
  
  max_to_end=@params.get_param('max_ab_to_end').to_i
  # type = 'ActionAbAdapter'
  actions=[]   
  adapter_size=0 
  
  #@stats['adapter_size']={}
  adapters.each do |c|                           # adds the correspondent action to the sequence 
    # puts "is the adapter near to the end of sequence ? #{c.q_end+seq.insert_start+max_to_end} >= ? #{seq.seq_fasta_orig.size-1}"   
      adapter_size=c.q_end-c.q_beg+1
      #if ((c.q_end+seq.insert_start+max_to_end)>=seq.seq_fasta_orig.size-1)  
      right_action = true
      #if ab adapter is very near to the end of original sequence
     if c.q_end>=seq.seq_fasta.length-max_to_end
        message = c.subject_id 
        type = 'ActionAbAdapter'
        ignore=false 
        add_stats('adapter_type','normal') 
      
      elsif (c.q_beg <= 4) && (adapter_size>=MIN_LEFT_ADAPTER_SIZE) #left adapter
        message = c.subject_id    
        type = 'ActionAbLeftAdapter'
        ignore = false
        right_action = false
        add_stats('adapter_type','left') 
      elsif (adapter_size>=MIN_FAR_ADAPTER_SIZE)
        message = c.subject_id    
        type = 'ActionAbFarAdapter'
        ignore = false
        add_stats('adapter_type','far') 
      else
        ignore=true 
      end 
      
      if !ignore
        a = seq.new_action(c.q_beg,c.q_end,type) 
        a.message = message 
        a.reversed = c.reversed 
        if right_action
          a.right_action = true    #mark as rigth action to get the left insert
        else
          a.left_action = true
        end
        actions.push a  
      
        # puts "adapter_size #{adapter_size}"

        #@stats[:adapter_size]={adapter_size => 1} 
        add_stats('adapter_size',adapter_size) 
        add_stats('adapter_id',message)
      end 
  end 
  
  if !actions.empty?
    seq.add_actions(actions)   
    add_stats('sequences_with_adapter','count')
  end
  
  
  #    
end

#execute(seqs) ⇒ Object

Begins the plugin1’s execution to warn that there are contaminants in the sequence “seq”



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# File 'lib/seqtrimnext/plugins/plugin_ab_adapters.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

#filter_hits(hits, end_pos) ⇒ Object

filter hits that are far the extreme and do not have a valid length



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# File 'lib/seqtrimnext/plugins/plugin_ab_adapters.rb', line 47

def filter_hits(hits,end_pos)
  hits.reverse_each do |hit|
   if (hit.q_end < (end_pos-40)) && ((hit.q_end-hit.q_beg+1)<(@params.get_ab_adapter(hit.subject_id).length*0.80).to_i)
     hits.delete(hit)
   #   puts "DELETE #{hit.inspect}"
   # else
   #   puts "ACCEPTED #{hit.inspect}, >= #{(@params.get_ab_adapter(hit.subject_id).length*0.2).to_i}"
   end
  end
  
end