Class: PluginSangerAdapters

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

Overview

Author: DGF y ABR

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_plugin_stats, #add_stats, #add_text_stats, auto_setup, #can_execute?, check_param, #execute, 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_sanger_adapters.rb', line 179

def self.check_params(params)
  errors=[]  
  
  comment='Blast E-value used as cut-off when searching for Sanger adapters'
  # default_value = 1e-6
  default_value = 1
  params.check_param(errors,'blast_evalue_sanger','Float',default_value,comment)
  
  comment='Minimum required identity (%) for a reliable Sanger adapter'
  default_value = 95
  params.check_param(errors,'blast_percent_sanger','Integer',default_value,comment)

  comment='Minimum required adapter size for a valid Sanger adapter'
  default_value = 10
  params.check_param(errors,'min_sanger_adapter_size','Integer',default_value,comment)
  
  comment='Path for Sanger adapters database'
  default_value = File.join($FORMATTED_DB_PATH,'adapters_sanger.fasta')
  params.check_param(errors,'adapters_sanger_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_sanger_adapters.rb', line 211

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_sanger_adapters.rb', line 202

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

.valid_graphs ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_sanger_adapters.rb', line 222

def self.valid_graphs
  return ['adapter_type']
end

Instance Method Details

#do_blasts(seqs) ⇒ Object 



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

def do_blasts(seqs)
   
   # find MIDS  with less results than max_target_seqs value 
   blast=BatchBlast.new("-db #{@params.get_param('adapters_sanger_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_sanger')} -word_size #{MIN_ADAPTER_SIZE}")  
   $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_sanger_adapters.rb', line 64

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 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)

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

  filter_adapters(adapters)

  if adapters.count==1 # only one adapter
    c=adapters.first
    adapter_size=c.q_end-c.q_beg+1
    message = c.subject_id 
    type = 'ActionSangerLeftAdapter'
    stat_type='left'
    add_stats('adapter_type',stat_type)

    a = seq.new_action(c.q_beg,c.q_end,type)
    a.message = message 
    a.reversed = c.reversed 
    a.left_action = true
    actions.push a
           
    add_stats('adapter_size',adapter_size) 
    add_stats('adapter_id',message)

  elsif adapters.count >=2
    type = 'ActionSangerLeftAdapter'
    stat_type='left'
    left_action=true
    right_action=false

    adapters.sort!{|a1,a2| a1.q_beg <=> a2.q_beg}
    old_qend=adapters.first.q_end
    
    max_slice_size=[]

    # left_qend=adapters.first.q_end
    adapters.each do |c|                           # adds the correspondent action to the sequence 


      # check if it is a right adapter
      if c.q_beg > (old_qend+50)
        type=type = 'ActionSangerRightAdapter'
        stat_type='right'
        left_action=false
        right_action=true
      end

      adapter_size=c.q_end-c.q_beg+1
      message = c.subject_id 
      add_stats('adapter_type',stat_type)

      a = seq.new_action(c.q_beg,c.q_end,type)
      a.message = message 
      a.reversed = c.reversed 
      a.left_action = left_action
      a.right_action = right_action

      # if action.last.q_end - a.start_pos > max_slice_size.last[:size]
      
      # end

      actions.push a
    
      add_stats('adapter_size',adapter_size)
      add_stats('adapter_id',message)

      old_qend=adapters.first.q_end

    end
    
  end    
  
  if !actions.empty?
    seq.add_actions(actions)
    add_stats('sequences_with_adapter','count')
  end

  
  #    
end

#filter_adapters(adapters) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_sanger_adapters.rb', line 50

def filter_adapters(adapters)

 min_size=@params.get_param('min_sanger_adapter_size').to_i
 adapters.reverse_each do |c|
   adapter_size=c.q_end-c.q_beg+1

   if adapter_size < min_size
     adapters.delete(c)
   end
 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_sanger_adapters.rb', line 40

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_sanger_adapter(hit.subject_id).length*0.80).to_i)
  #  if ((hit.q_end-hit.q_beg+1)<(@params.get_sanger_adapter(hit.subject_id).length*0.80).to_i)
  #    hits.delete(hit)
  #  end
  # end
  
end