Class: BioDSL::Fasta

Inherits:
Object
  • Object
show all
Defined in:
lib/BioDSL/fasta.rb

Defined Under Namespace

Classes: IO

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(io) ⇒ Fasta

Returns a new instance of Fasta.



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# File 'lib/BioDSL/fasta.rb', line 60

def initialize(io)
  @io        = io
  @seq_name  = nil
  @seq       = ""
  @got_first = nil
  @got_last  = nil
end

Instance Attribute Details

#seq ⇒ Object

Returns the value of attribute seq.



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# File 'lib/BioDSL/fasta.rb', line 58

def seq
  @seq
end

#seq_name ⇒ Object

Returns the value of attribute seq_name.



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# File 'lib/BioDSL/fasta.rb', line 58

def seq_name
  @seq_name
end

Class Method Details

.open(*args) ⇒ Object 



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# File 'lib/BioDSL/fasta.rb', line 32

def self.open(*args)
  ios = IO.open(*args)

  if block_given?
    begin
      yield self.new(ios)
    ensure
      ios.close
    end
  else
    return self.new(ios)
  end
end

.read(*args) ⇒ Object 



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# File 'lib/BioDSL/fasta.rb', line 46

def self.read(*args)
  entries = []

  Fasta.open(*args) do |ios|
    ios.each do |entry|
      entries << entry
    end
  end

  entries
end

Instance Method Details

#each ⇒ Object 



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# File 'lib/BioDSL/fasta.rb', line 68

def each
  while entry = next_entry
    yield entry
  end
end

#next_entry ⇒ Object

Method to get the next FASTA entry form an ios and return this as a Seq object. If no entry is found or eof then nil is returned.



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# File 'lib/BioDSL/fasta.rb', line 80

def next_entry
  @io.each do |line|
    line.chomp!

    next if line.empty?

    if line[0] == '>'
      if not @got_first and not @seq.empty?
        raise FastaError, "Bad FASTA format -> content before Fasta header: #{@seq}" unless @seq.empty?
      end

      @got_first = true

      if @seq_name
        entry     = Seq.new(seq_name: @seq_name, seq: @seq)
        @seq_name = line[1 .. -1]
        @seq      = ""

        raise FastaError, "Bad FASTA format -> truncated Fasta header: no content after '>'" if @seq_name.empty?

        return entry
      else
        @seq_name = line[1 .. -1]

        raise FastaError, "Bad FASTA format -> truncated Fasta header: no content after '>'" if @seq_name.empty?
      end
    else
      @seq << line
    end
  end

  if @seq_name
    @got_last = true
    entry     = Seq.new(seq_name: @seq_name, seq: @seq)
    @seq_name = nil
    return entry
  end

  if not @got_last and not @seq.empty?
    raise FastaError, "Bad FASTA format -> content witout Fasta header: #{@seq}"
  end

  nil
end

#puts(*args) ⇒ Object 



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# File 'lib/BioDSL/fasta.rb', line 74

def puts(*args)
  @io.puts(*args)
end