Class: FastaQualFile

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_fasta/fasta_qual_file.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fasta_file_name, qual_file_name = '', qual_to_array = false) ⇒ FastaQualFile

Initialize instance



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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 24

def initialize(fasta_file_name,qual_file_name='',qual_to_array=false)

	
	if !File.exist?(fasta_file_name)
  	raise "File #{fasta_file_name} doesn't exists" 
	end
	
	@with_qual = true
	
	if qual_file_name.nil? or qual_file_name.empty? or !File.exist?(qual_file_name)
		@with_qual = false
    #raise "File #{qual_file_name} doesn't exists" 
	end
# puts "With_qual #{fasta_file_name}?: #{@with_qual}"
		
    @num_seqs = 0 ;      
    
    @seq_name = '';      
    @seq_comment='';
    @file_fasta = File.open(fasta_file_name) ;
    @end_fasta=false;
    
    if @with_qual  		
    
      @qual_to_array = qual_to_array

     @seq_qual_name='';
     @file_qual = File.open(qual_file_name) ;
     @end_qual=false;
    end
    
end

Instance Attribute Details

#end_fasta ⇒ Object

Returns the value of attribute end_fasta.



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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 19

def end_fasta
  @end_fasta
end

#num_seqs ⇒ Object

Returns the value of attribute num_seqs.



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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 19

def num_seqs
  @num_seqs
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 57

def close
    @file_fasta.close
    
    @file_qual.close if @with_qual
end

#each ⇒ Object

Scans all sequences



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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 67

def each
      
  rewind

 n,f,q,c = next_seq
  while (!n.nil?)
 
			if @with_qual

				yield(n,f,q,c)
			else
			  yield(n,f,q)
			end
			
				n,f,q,c=next_seq
  end

	rewind
	
end

#next_seq ⇒ Object

Scans a file, firing events to process content



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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 109

def next_seq
  
  #init variables
  res = nil
  
 # envia on_process_sequence
  if ((!@end_fasta) && (!@with_qual or !@end_qual))

     name_f,fasta,comment=read_fasta 
	    
      if @with_qual
			  
			  name_q,qual=read_qual 
			  
          if (name_f!=name_q)
					 raise DifferentNamesException.new, "Sequence(<#{name_f}>) and qual(<#{name_q}>) names differs. Sequence will be ignored."
           else
					@num_seqs=@num_seqs+1
		
					#storage a string of qualities in an array of qualities
		 	    # a_qual = qual.strip.split(/\s/).map{|e| e.to_i}
					# if ((!a_qual.nil?) && (!a_qual.empty?) && (fasta.size==a_qual.size))						

					if fasta.length == qual.count(' ') + 1
						if @qual_to_array
							a_qual = qual.strip.split(/\s/).map{|e| e.to_i}
							res =[name_f,fasta,a_qual,comment]
						else
							res =[name_f,fasta,qual,comment]
						end
				
					else #if (!a_qual.empty?)
						 raise DifferentSizesException.new,  "Sequence(<#{name_f}>) and qual(<#{name_q}>) sizes differs (#{fasta.length},#{qual.count(' ')} ). Sequence will be ignored."
					end 
				 
          end
		 
      else # without qual				 
		 		res =[name_f,fasta,comment]
      end
  end
	
	return res
end

#rewind ⇒ Object 



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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 89

def rewind
   
   @num_seqs = 0 ;      
   
   @seq_name = '';      
   @seq_comment= '';
   @file_fasta.pos=0
   @end_fasta=false;

   if @with_qual
		 @seq_qual_name='';
		 @file_qual.pos=0
		 @end_qual=false;   
   end
  
end

#with_qual? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scbi_fasta/fasta_qual_file.rb', line 154

def with_qual?
  @with_qual
end