Summary

Bio::Assembly::IO - Handler for Assembly::IO Formats

Package variables

Inherit

Bio::Root::IO Bio::Root::Root

Synopsis

    use Bio::Assembly::IO;

    $in  = Bio::Assembly::IO->new(-file=>"'phrap');
    $out = Bio::Assembly::IO->new(-file=>">outputfilename",
                                  -format=>'phrap');

    while ( my $seq = $in->next_seq() ) {
       $out->write_seq($seq);
    }

Description

Bio::Assembly::IO is a handler module for formats in the Assembly::IO set
(e.g. Bio::Assembly::IO::phrap).

Methods

Methods description

 Title   : new
 Usage   : Bio::Assembly::IO->new(-file =>$filename,-format=>'format')
 Function: Returns a new assembly stream
 Returns : A Bio::Assembly::IO::Handler initialised
           with the appropriate format
 Args    : -file => $filename
           -format => format

 Title   : next_assembly
 Usage   : $cluster = $stream->next_assembly()
 Function: Reads the next assembly object from the stream and returns it.
 Returns : a Bio::Assembly::ScaffoldI compliant object
 Args    : none

 Title   : _load_format_module
 Usage   : *INTERNAL Assembly::IO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function: guess format based on file suffix
 Example :
 Returns : guessed format of filename (lower case)
 Args    :
 Notes   : formats that _filehandle() will guess includes
           only phrap, by now.

Methods code

sub new {

    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;

    # or do we want to call SUPER on an object if $caller is an
    # object?
    if( $class =~ /Bio::Assembly::IO::(\S+)/ ) {
	my ($self) = $class->SUPER::new(@args);
	$self->_initialize(@args);
	return $self;
    } else {

	my %param = @args;
	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys

	$class->throw("Need at least a file name to proceed!")
	    unless (defined $param{'-file'} || defined $ARGV[0]);

	my $format = $param{'-format'} ||
	    $class->_guess_format( $param{-file} || $ARGV[0] );
	$format = "\L$format";	# normalize capitalization to lower case

	# normalize capitalization
	return unless( $class->_load_format_module($format) );
	return "Bio::Assembly::IO::$format"->new(@args);
    }

}

sub _initialize {

    my($self, @args) = @_;
    # initialize the IO part
    $self->_initialize_io(@args);

}

sub next_assembly {

   my ($self, $seq) = @_;
   $self->throw("Sorry, you cannot read from a generic Bio::Assembly::IO object.");

}

sub _load_format_module {

  my ($self,$format) = @_;
  my $module = "Bio::Assembly::IO::" . $format;
  my $ok;

  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END
$self: could not load $format - for more details on supported formats please see the Assembly::IO docs
Exception $@
END
  ;
  }
  return $ok;

}

sub _guess_format {

   my $class = shift;
   my $arg   = shift;

   return unless defined($arg);
   return 'ace' if ($arg =~ /\.ace\.\d+$/i);
   return 'phrap' if ($arg =~ /\.phrap\.out$/i);

}

sub DESTROY {

    my $self = shift;

    $self->close();

}

sub TIEHANDLE {

    my ($class,$val) = @_;
    return bless {'seqio' => $val}, $class;

}

sub READLINE {

  my $self = shift;
  return $self->{'seqio'}->next_seq() unless wantarray;
  my (@list, $obj);
  push @list, $obj while $obj = $self->{'seqio'}->next_seq();
  return @list;

}

sub PRINT {

  my $self = shift;
  $self->{'seqio'}->write_seq(@_);

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Robson Francisco de Souza
E-mail: rfsouza@citri.iq.usp.br

#

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _