| Bio::SeqIO::bsml_sax(3pm) | User Contributed Perl Documentation | Bio::SeqIO::bsml_sax(3pm) |
Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX
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);
In addition to parts of the Bio:: hierarchy, this module uses: XML::SAX
This object can transform Bio::Seq objects to and from BSML (XML) flatfiles.
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
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.
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
Email jason-at-bioperl-dot-org
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 :
| 2018-10-27 | perl v5.26.2 |