| Bio::SeqIO::gbxml(3pm) | User Contributed Perl Documentation | Bio::SeqIO::gbxml(3pm) |
Bio::SeqIO::gbxml - GenBank 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 GenBank XML file:
$stream = Bio::SeqIO->new( -file => $filename, -format => 'gbxml');
while ( my $bioSeqObj = $stream->next_seq() ) {
# do something with $bioSeqObj
}
To write a Seq object to the current file handle in GenBank XML format:
$stream->write_seq( -seq => $seqObj);
If instead you would like a XML::DOM object containing the GBXML, 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 GenBank 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
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 golharam-at-umdnj-dot-edu
Title : next_seq Usage : my $bioSeqObj = $stream->next_seq Function: Retrieves the next sequence from a SeqIO::gbxml stream. Returns : A reference to a Bio::Seq::RichSeq object Args :
| 2018-10-27 | perl v5.26.2 |