Summary

Bio::SeqIO::strider - DNA strider sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

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 strider
'binary' format, as documented in the strider manual, in which the
first 112 bytes are a header, following by the sequence, followed by a
sequence description.
Note: it does NOT assign any sequence identifier, since they are not
contained in the byte stream of the file; the Strider application
simply displays the name of the file on disk as the name of the
sequence. The caller should set the id, probably based on the name of
the file (after possibly cleaning up whitespace, which ought not to be
used as the id in most applications).
Note: the strider 'comment' is mapped to the BioPerl 'description'
(since there is no other text field, and description maps to defline
text).

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq 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    : array of 1 to n Bio::PrimarySeqI objects

Methods code

sub _initialize {

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

}

sub next_seq {

  my( $self ) = @_;
  my $fh =  $self->_fh;
  my ($header,$sequence,$fulldesc);
  read $fh,$header,$size_F_HEADER or return ; #don't die here with "could not read header: $@" !!!;
  $self->throw("required $size_F_HEADER bytes while reading strider header in " . $self->{'_file'} . " but found: " . length($header))  
    unless $size_F_HEADER == length($header);
  my $headerdata = $c->unpack('F_HEADER',$header) or return;
  read $fh,$sequence,$headerdata->{nLength};
  read $fh,$fulldesc,$headerdata->{com_length};
  $fulldesc =~ s/\cM/ /g;	# gratuitous replacement of mac
                                # linefeed with space.
  my $seq = $self->sequence_factory->create(
					    # -id          => $main::ARGV, #might want to set this in caller to $ARGV.
					    -seq         => $sequence,
					    -desc        => $fulldesc,
					    -alphabet    => $type2alphabet{$headerdata->{type}} || 'dna',
					   );

  return $seq;

}

sub write_seq {

  my ($self,@seq) = @_;
  my $fh =  $self->_fh() || *STDOUT; #die "could not determine filehandle in strider.pm";
  foreach my $seq (@seq) {
    $self->throw("Did not provide a valid Bio::PrimarySeqI object") 
      unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
    my  $headerdata = $c->pack('F_HEADER',{
					   versionNb   => 0, 
					   type        => $alphabet2type{$seq->alphabet} || $alphabet2type{dna},
					   topology    => $seq->is_circular ? 1 : 0,
					   nLength     => $seq->length,
					   nMinus      => 0,
					   com_length  => length($seq->desc || ""),
					  });
    print $fh $headerdata, $seq->seq() || "" , $seq->desc || "";
  }

}

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/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/

Email: mec@stowers-institute.org

Modelled after Bio::SeqIO::fasta by Ewan Birney <birney@ebi.ac.uk> and
Lincoln Stein <lstein@cshl.org>

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