Bio::SeqIO::bsml_sax(3pm) User Contributed Perl Documentation 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:
https://redmine.open-bio.org/projects/bioperl/
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 :
perl v5.14.2 2012-03-02 Bio::SeqIO::bsml_sax(3pm)