Class: ScanForRestrSite

Inherits:
Object
  • Object
show all
Defined in:
lib/seqtrimnext/classes/scan_for_restr_site.rb

Overview

Author

Almudena Bocinos Rioboo

This class provided the methods to read the parameter’s file and to create the structure where will be storaged the param’s name and the param’s numeric-value

Instance Method Summary collapse

Constructor Details

#initialize(sequence, rest) ⇒ ScanForRestrSite

Creates the structure and start the reading of parameter’s file



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# File 'lib/seqtrimnext/classes/scan_for_restr_site.rb', line 10

def initialize(sequence,rest)    
  @seq_fasta=sequence 
  @rest=rest      
  puts "#{@seq_fasta}  , #{@rest}"  
  res = execute
  

  res.each do |e| 
      puts "#{e.join(',')}"
  end
  
# selects from res,the max good hit  
  puts "--- MAX: --- "
  
  max = res.max{|e1,e2| e1[1]<=> e2[1]}
                    
  puts max.join(' ; ')                    
                                           
# checks if the max one has the size of restriction with a margen error
  margen = (@rest.size <= 4)? 0 : 1;  # <- don't change       
  if ((max[1] !=  @rest.size) && (max[1] != @rest.size-margen)) 
    puts "-the max good hit hasn't the size minimum: #{@rest.size} or #{@rest.size-margen} "
    max=[]
  end
  
  
  
  #read_file(path)   
end

Instance Method Details

#execute ⇒ Object 



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# File 'lib/seqtrimnext/classes/scan_for_restr_site.rb', line 42

def execute    
  r=[]
                            # 
                            # for (my $p=0; $p < $sL-$srfL; $p++){
                            #     $os = $ns = $xs = 0;
                            #     for ( my $i=0; $i < $srfL; $i++ ) {
                            #         my $c  = substr($s, $i+$p, 1);  # ver si decrementar antes pos
                            #         my $cc = substr($restrSite, $i, 1);
                            #         if ($c eq $cc) {
                            #             ++$os;
                            #         } elsif ($c eq "N"){
                            #             ++$ns;
                            #         } else {
                            #             ++$xs;
                            #         }
                            #     }
                            #     $r[$p] = [$p, $os, $ns, $xs];
                            #         print "$p, $os, $ns, $xs\n";
                            # }                     
  for p in 0..@seq_fasta.size-@rest.size 
      os = 0; 
      ns = 0; 
      xs = 0;                    
      puts "-------[#{p}]-#{@seq_fasta[p,@seq_fasta.size-p]}  , #{@rest}"  
      
     i=0
    @rest.each_char do |cc|
       c = @seq_fasta[i+p].chr
       puts "(#{c}==#{cc})=>#{c==cc}"
      if (c == cc)
        os += 1
      elsif (c == 'N')
        ns += 1
      else     
        xs += 1
      end
      i+=1     
      
    end
    r[p]=[p,os,ns,xs]
     puts r[p].join(',')
  end     
  return r
end

#exists?(param_name) ⇒ Boolean

Returns true if exists the parameter and nil if don’t

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/classes/scan_for_restr_site.rb', line 131

def exists?(param_name)
  return !@h[param_name].nil?
end

#get_param(param) ⇒ Object

Return the parameter’s list in an array



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# File 'lib/seqtrimnext/classes/scan_for_restr_site.rb', line 119

def get_param(param)
  #$LOG.debug "Get Param:  #{@h[param]}"
  return @h[param]
end

#print_parameters ⇒ Object

Prints the pair name/numeric-value for every parameter



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# File 'lib/seqtrimnext/classes/scan_for_restr_site.rb', line 111

def print_parameters()
  @h.each do |clave, valor|
    
    $LOG.debug  "The Parameter #{clave} have the value " +valor.to_s
  end
end

#read_file(path_fichero) ⇒ Object

Reads param’s file



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# File 'lib/seqtrimnext/classes/scan_for_restr_site.rb', line 88

def read_file(path_fichero)
  File.open(path_fichero).each_line do |line| 
         
    line.chomp! # delete end of line      
    
    if !line.empty?
      if !(line =~ /^#/)   # if line is not a comment
        # extract the parameter's name in params[0] and the parameter's value in params[1]
        params = line.split(/\s*=\s*/)
        
        # storage in the hash the pair key/value, in our case will be name/numeric-value , 
        # that are save in params[0] and params[1],  respectively
        @h[params[0]] = params[1]
        
        $LOG.debug "read: #{params[1]}"
      end # end if comentario
    end #end if line
  end #end each
  $LOG.info "File Params have been readed"

end

#set_param(param, value) ⇒ Object 



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# File 'lib/seqtrimnext/classes/scan_for_restr_site.rb', line 124

def set_param(param,value)
  @h[param] = value
end