Class: FastaFile

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

Overview

Author: Almudena Bocinos Rioboo

Use: Deprecated. The class FastaReader has been substituted by FastaQualReader

Reads a fasta file and fires events to process it

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(file_name) ⇒ FastaFile

Initialize instance



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# File 'lib/scbi_fasta/fasta_file.rb', line 14

def initialize(file_name)
  if File.exist?(file_name)
  @num_seqs = 0

  @file_name = file_name
  @file = File.open(file_name)
else
		raise "File #{file_name} doesn't exists" 
  	
  end
  
end

Instance Attribute Details

#num_seqs ⇒ Object (readonly)

Returns the value of attribute num_seqs.



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# File 'lib/scbi_fasta/fasta_file.rb', line 10

def num_seqs
  @num_seqs
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/scbi_fasta/fasta_file.rb', line 84

def close
	@file.close
end

#each ⇒ Object

Scans a file, firing events to process content



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# File 'lib/scbi_fasta/fasta_file.rb', line 29

def each
  
  #init variables
  seq_name = '';
  seq_fasta = '';
  seq_found = false;

  
  # for each line of the file
  @file.each do |line|
    
    line.chomp!;
    # if line is name
    if line =~ /^>/
      
      #process previous sequence
      if seq_found
     @num_seqs=@num_seqs+1
        yield(seq_name,seq_fasta);
      end
      
      #get only name

   #get only name
     line.gsub!(/^>\s*/,'');
    
     line =~ /(^[^\s]+)/

     # remove comments
     seq_name = $1

      seq_fasta='';
      seq_found = true;
      
    else

    line.strip! if !line.empty?
	
      #add line to fasta of seq
      seq_fasta+=line;

    seq_fasta.strip! if !seq_fasta.empty?

    end
      
  end

  # when found EOF, process last sequence
  if seq_found
			@num_seqs=@num_seqs+1
    yield(seq_name,seq_fasta);
  end
end

#with_qual? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scbi_fasta/fasta_file.rb', line 88

def with_qual?
  false
end