class PluginAbAdapters

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginAdapters

Inherit: Plugin

Constants

MIN_ADAPTER_SIZE

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

MIN_FAR_ADAPTER_SIZE
MIN_LEFT_ADAPTER_SIZE

Public Class Methods

check_params(params) click to toggle source

Returns an array with the errors due to parameters are missing

# File lib/seqtrimnext/plugins/plugin_ab_adapters.rb, line 180
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) click to toggle source
# File lib/seqtrimnext/plugins/plugin_ab_adapters.rb, line 212
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) click to toggle source
# File lib/seqtrimnext/plugins/plugin_ab_adapters.rb, line 203
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() click to toggle source
# File lib/seqtrimnext/plugins/plugin_ab_adapters.rb, line 223
def self.valid_graphs
  return ['adapter_type']
end

Public Instance Methods

do_blasts(seqs) click to toggle source
# File lib/seqtrimnext/plugins/plugin_ab_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_ab_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_ab')} -word_size #{MIN_ADAPTER_SIZE}")  

   # con culling limit hay situaciones en las que un hit largo con 1 mismatch es ignorado porque hay otro más corto que no tiene ningun error, no es aceptable.
   #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} -culling_limit=1")
   $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)
   #blast_table_results = BlastTableResult.new(blast_table_results)

   
   t1=Time.now
   blast_table_results = blast.do_blast(fastas,:table,false)
   add_plugin_stats('execution_time','blast',Time.now-t1)

   
   #f=File.new("/tmp/salida_#{fastas.first.gsub('>','').gsub('/','_')}.blast",'w+')
   #f.puts blast.get_blast_cmd
   #f.puts blast_table_results
   #f.close

   t1=Time.now
   blast_table_results = BlastTableResult.new(blast_table_results)
   add_plugin_stats('execution_time','parse',Time.now-t1)


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

   # t1=Time.now
   # blast_table_results = BlastStreamxmlResult.new(blast_table_results)
   # add_plugin_stats('execution_time','parse',Time.now-t1)
   
   # puts blast_table_results.inspect
  
   return blast_table_results
end
exec_seq(seq,blast_query) click to toggle source
# File lib/seqtrimnext/plugins/plugin_ab_adapters.rb, line 80
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)

   # 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
filter_hits(hits,end_pos) click to toggle source

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

# File lib/seqtrimnext/plugins/plugin_ab_adapters.rb, line 68
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