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Bio::SeqIO::bsml_sax.3pm

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
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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    :