bio::seqio::gbxml(3pm) [debian man page]

Bio::SeqIO::gbxml(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::gbxml(3pm)

NAME

       Bio::SeqIO::gbxml - GenBank 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 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);

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 GenBank 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

   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 - Ryan Golhar
       Email golharam-at-umdnj-dot-edu

METHODS

   next_seq
       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	 :

perl v5.14.2							    2012-03-02						    Bio::SeqIO::gbxml(3pm)

Bio::SeqIO::alf(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::alf(3pm)

NAME

       Bio::SeqIO::alf - alf trace sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform Bio::Seq objects to and from alf trace files.

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/

AUTHORS - Aaron Mackey
       Email: amackey@virginia.edu

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq::Quality object
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: Bio::Seq object

perl v5.14.2							    2012-03-02						      Bio::SeqIO::alf(3pm)