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Summary

Bio::SeqIO::ztr - ztr trace sequence input/output stream

Package variables

Included modules

Synopsis

Do not use this module directly. Use it via the Bio::SeqIO class.

Description

This object can transform Bio::Seq objects to and from ztr trace
files.

Methods

Methods description

 Title   : compression
 Usage   : $stream->compression(3);
 Function: determines the level of ZTR compression
 Returns : the current (or newly set) value.
 Args    : 1, 2 or 3 - any other (defined) value will cause the compression
           to be reset to the default of 2.

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::SeqWithQuality object
 Args    : NONE

 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq object

Methods code

sub BEGIN {

    eval { require Bio::SeqIO::staden::read; };
    if ($@) {
	$READ_AVAIL = 0;
    } else {
	push @ISA, "Bio::SeqIO::staden::read";
	$READ_AVAIL = 1;
    }

}

sub _initialize {

  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);  
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::Seq::SeqWithQuality'));      
  }

  my ($compression) = $self->_rearrange([qw[COMPRESSION]], @args);
  $compression = 2 unless defined $compression;
  $self->compression($compression);

  unless ($READ_AVAIL) {
      Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
			      -text  => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
			    );
  }

}

sub compression {

    my ($self, $val) = @_;

    if (defined $val) {
	if ($val =~ m/^1|2|3$/o) {
	    $self->{_compression} = $val;
	} else {
	    $self->{_compression} = 2;
	}
    }

    return $self->{_compression};
}

1;

}

sub next_seq {

    my ($self) = @_;

    my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'ztr');

    # create the seq object
    $seq = $self->sequence_factory->create(-seq        => $seq,
					   -id         => $id,
					   -primary_id => $id,
					   -desc       => $desc,
					   -alphabet   => 'DNA',
					   -qual       => $qual
					   );
    return $seq;

}

sub write_seq {

    my ($self,@seq) = @_;

    my $fh = $self->_fh;
    foreach my $seq (@seq) {
	$self->write_trace($fh, $seq, 'ztr' . $self->compression);
    }

    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 1;

}

General documentation

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

  bioperl-l@bioperl.org            - General discussion
  http://bioperl.org/MailList.shtml - 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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email: amackey@virginia.edu

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