Christopher Fields > BioPerl > Bio::SeqIO::bsml_sax

Download:
BioPerl-1.6.924.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Module Version: 1.006924   Source  

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:

  https://github.com/bioperl/bioperl-live/issues

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    :
syntax highlighting: