Class: PluginIgnoreRepeated

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

Constant Summary collapse

SIZE_SEARCH_IN_IGNORE = 
15

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



89
90
91
92
93
94
95
96
97
98
 
# File 'lib/seqtrimnext/plugins/plugin_ignore_repeated.rb', line 89

def self.check_params(params)
  errors=[]
                
   # self.check_param(errors,params,'fasta_file_input','String')
   self.check_param(errors,params,'blast_evalue_ignore_repeated','Float') 
   self.check_param(errors,params,'blast_percent_ignore_repeated','Integer')
   self.check_param(errors,params,'piro_repeated_start','Integer')
   self.check_param(errors,params,'piro_repeated_length','Integer')
  return errors
end

Instance Method Details

#exec_seq(seq) ⇒ Object 



23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
 
# File 'lib/seqtrimnext/plugins/plugin_ignore_repeated.rb', line 23

def exec_seq(seq)
  $LOG.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: searching sequence repeated at input file" 

  fasta_input=@params.get_param('truncated_input_file')
  
  blast = BatchBlast.new("-db #{fasta_input}" ,'blastn'," -task blastn-short -searchsp #{SIZE_SEARCH_IN_IGNORE} -evalue #{@params.get_param('blast_evalue_ignore_repeated')} -perc_identity #{@params.get_param('blast_percent_ignore_repeated')}")  #get contaminants
  
  p_start = @params.get_param('piro_repeated_start').to_i
  p_length = @params.get_param('piro_repeated_length').to_i
  
  
  blast_table_results = blast.do_blast(seq.seq_fasta[p_start,p_length])             #rise seq to contaminants  executing over blast
  
  #blast_table_results = BlastTableResult.new(res)
  
 
   type = "ActionIgnoreRepeated"        
   
   # @stats[:rejected_seqs]={}    
     
   actions=[]     
   blast_table_results.querys.each do |query|
                                             
         # puts "BLAST IGUALES:"
         # puts res.join("\n")       
     if query.size>1   
       names = query.hits.collect{ |h| 
            if h.align_len > (p_length-2)
              h.subject_id
            end
       }
           
       names.compact!   
        
        # puts "IGUALES:" + names.size.to_s 
        #            puts names.join(',')               
        
        if !names.empty?
           names.sort!
         
           if (names[0] != seq.seq_name)   # Add action when the sequence  is repeated 
         #  if true 
            a = seq.new_action(0,0,type)
            a.message = seq.seq_name  + ' equal to ' + names[0]    
            actions.push a
            seq.seq_rejected=true   
            seq.seq_rejected_by_message='repeated'
            seq.seq_repeated=true       
            
              # @stats[:rejected_seqs]={'rejected_seqs_by_repe' => 1}   
              add_stats('rejected_seqs','rejected_seqs_by_repe') 
               # puts "#{names[0]} != #{seq.seq_name} >>>>>>"       
         end                                                               
       end
       
     end       
     
   end 
   
   seq.add_actions(actions)
   
end

#execute(seqs) ⇒ Object

Begins the plugin1’s execution to warn that there are repeated sequences, and disables all but one“



16
17
18
19
20
 
# File 'lib/seqtrimnext/plugins/plugin_ignore_repeated.rb', line 16

def execute(seqs)
  seqs.each do |s|
    exec_seq(s)
  end
end