Sendu Bala
and 1 contributors

NAME

Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX

SYNOPSIS

 It is probably best not to use this object directly, but rather go
 through the SeqIO handler system. To read a BSML file:

    $stream = Bio::SeqIO->new( -file => $filename, -format => 'bsml');

    while ( my $bioSeqObj = $stream->next_seq() ) {
        # do something with $bioSeqObj
    }

 To write a Seq object to the current file handle in BSML XML format:

    $stream->write_seq( -seq => $seqObj);

 If instead you would like a XML::DOM object containing the BSML, use:

    my $newXmlObject = $stream->to_bsml( -seq => $seqObj);

DEPENDENCIES

 In addition to parts of the Bio:: hierarchy, this module uses:

 XML::SAX

DESCRIPTION

 This object can transform Bio::Seq objects to and from BSML (XML)
 flatfiles.

FEEDBACK

Mailing Lists

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

Reporting Bugs

 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/

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

METHODS

next_seq

 Title   : next_seq
 Usage   : my $bioSeqObj = $stream->next_seq
 Function: Retrieves the next sequence from a SeqIO::bsml stream.
 Returns : A reference to a Bio::Seq::RichSeq object
 Args    :