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 :