Exemplo n.º 1
0
class FastaIterator(InputFile):
    def __init__(self, name=""):
        self.init()
        # initialize
        if (name != ""):
            self.setName(name)
            self.open()
        self.fasta = None

    def nextHeader(self):
        # Find the start of the next sequence.
        while ( ( self.isEndOfFile () == 0 ) and \
                ( self.line != "" ) and \
                ( self.line [ 0 ] != '>' ) ):
            self.next()
        return self.line

    def nextSequence(self):
        self.nextHeader()

        # Parse the header line.
        self.fasta = FastaSequence()
        self.fasta.parseHeader(self.line)

        # Read in the sequence data.
        self.next()
        seq = ""
        while ( ( self.isEndOfFile () == 0 ) and \
                ( self.line != "" ) and
                ( self.line [ 0 ] != '>' ) ):
            seq = seq + string.rstrip(self.line)
            self.next()
        self.fasta.setSequence(seq)
        return self.fasta
Exemplo n.º 2
0
class FastaIterator ( InputFile ):

  def __init__ ( self, name = "" ):
    self.init ();		# initialize
    if ( name != "" ):
      self.setName ( name )
      self.open ()
    self.fasta = None

  def nextHeader ( self ):
    # Find the start of the next sequence.
    while ( ( self.isEndOfFile () == 0 ) and \
            ( self.line != "" ) and \
            ( self.line [ 0 ] != '>' ) ):
      self.next ()
    return self.line

  def nextSequence ( self ):
    self.nextHeader ()

    # Parse the header line.
    self.fasta = FastaSequence ()
    self.fasta.parseHeader ( self.line )

    # Read in the sequence data.
    self.next ()
    seq = ""
    while ( ( self.isEndOfFile () == 0 ) and \
            ( self.line != "" ) and
            ( self.line [ 0 ] != '>' ) ):
      seq = seq + string.rstrip ( self.line )
      self.next ()
    self.fasta.setSequence ( seq )
    return self.fasta
Exemplo n.º 3
0
class FastaIterator ( InputFile ):

  #############################################################################
  #
  # FastaIterator constructor.
  #
  def __init__ ( self, name = "" ):
    self.initialize ();		# initialize
    if ( name != "" ):
      self.setFileName ( name )
      self.openFile ()
    self.fasta = None


  #############################################################################
  #
  # This method reads the FASTA sequence library file to the next header line.
  #
  def nextHeader ( self ):
    # Find the start of the next sequence.
    while ( ( self.isEndOfFile () == 0 ) and \
            ( self.line != "" ) and \
            ( self.line [ 0 ] != '>' ) ):
      self.nextLine ()
    return self.line


  #############################################################################
  #
  # This method returns the next FastaSequence sequence object.
  #
  def nextSequence ( self ):
    self.nextHeader ()

    # Parse the header line.
    self.fasta = FastaSequence ()
    self.fasta.parseHeader ( self.line )

    # Read in the sequence data.
    self.nextLine ()
    seq = ""
    while ( ( self.isEndOfFile () == 0 ) and \
            ( self.line != "" ) and
            ( self.line [ 0 ] != '>' ) ):
      seq = seq + self.line.rstrip ()
      self.nextLine ()
    self.fasta.setSequence ( seq )
    return self.fasta
Exemplo n.º 4
0
class FastaIterator(InputFile):

    #############################################################################
    #
    # FastaIterator constructor.
    #
    def __init__(self, name=""):
        self.initialize()
        # initialize
        if (name != ""):
            self.setFileName(name)
            self.openFile()
        self.fasta = None

    #############################################################################
    #
    # This method reads the FASTA sequence library file to the next header line.
    #
    def nextHeader(self):
        # Find the start of the next sequence.
        while ( ( self.isEndOfFile () == 0 ) and \
                ( self.line != "" ) and \
                ( self.line [ 0 ] != '>' ) ):
            self.nextLine()
        return self.line

    #############################################################################
    #
    # This method returns the next FastaSequence sequence object.
    #
    def nextSequence(self):
        self.nextHeader()

        # Parse the header line.
        self.fasta = FastaSequence()
        self.fasta.parseHeader(self.line)

        # Read in the sequence data.
        self.nextLine()
        seq = ""
        while ( ( self.isEndOfFile () == 0 ) and \
                ( self.line != "" ) and
                ( self.line [ 0 ] != '>' ) ):
            seq = seq + self.line.rstrip()
            self.nextLine()
        self.fasta.setSequence(seq)
        return self.fasta
Exemplo n.º 5
0
    def nextSequence(self):
        self.nextHeader()

        # Parse the header line.
        self.fasta = FastaSequence()
        self.fasta.parseHeader(self.line)

        # Read in the sequence data.
        self.nextLine()
        seq = ""
        while ( ( self.isEndOfFile () == 0 ) and \
                ( self.line != "" ) and
                ( self.line [ 0 ] != '>' ) ):
            seq = seq + self.line.rstrip()
            self.nextLine()
        self.fasta.setSequence(seq)
        return self.fasta
Exemplo n.º 6
0
  def nextSequence ( self ):
    self.nextHeader ()

    # Parse the header line.
    self.fasta = FastaSequence ()
    self.fasta.parseHeader ( self.line )

    # Read in the sequence data.
    self.nextLine ()
    seq = ""
    while ( ( self.isEndOfFile () == 0 ) and \
            ( self.line != "" ) and
            ( self.line [ 0 ] != '>' ) ):
      seq = seq + self.line.rstrip ()
      self.nextLine ()
    self.fasta.setSequence ( seq )
    return self.fasta