debian man page for bio::seqio::flybase_chadoxml

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

NAME
       Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream

SYNOPSIS
       It is probably best not to use this object directly, but rather go through the SeqIO handler system:

	   $writer = Bio::SeqIO->new(-file => ">chado.xml",
				     -format => 'flybase_chadoxml');

	   # assume you already have Sequence or SeqFeature objects
	   $writer->write_seq($seq_obj);

	   #after writing all seqs
	   $writer->close_chadoxml();

DESCRIPTION
       This is a simple subclass of Bio::SeqIO::chadoxml; please see its documentation for details.

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 - Peili Zhang
       Email peili@morgan.harvard.edu

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

   return_ftype_hash
	Title	 : return_ftype_hash
	Usage	 : $obj->return_ftype_hash()
	Function : A simple hash where returning it has be factored out of the main
		   code to allow subclasses to override it.
	Returns  : A hash that indicates what the name of the SO term is and what
		   the name of the Sequence Ontology is in the cv table.
	Args	 : The string that represents the SO term.
	Status	 :

   return_reltypename
	Title	 : return_reltypename
	Usage	 : $obj->return_reltypename
	Function : Return the appropriate relationship type name depending on the
		   feature type (typically part_of, but derives_from for polypeptide).
	Returns  : A relationship type name.
	Args	 : A SO type name.
	Status	 :

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype,
			 -src_feature=>$srcfeature,
			 -src_feat_type=>$srcfeattype,
			 -nounflatten=>0 or 1,
			 -is_analysis=>'true' or 'false',
			 -data_source=>$datasource)
	Function: writes the $seq object (must be seq) into chadoxml.
	Returns : 1 for success and 0 for error
	Args	 : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature,
		   $srcfeattype, $nounflatten, $is_analysis and $data_source.

       Overrides Bio::SeqIO::chadoxml's write_seq method just to add an internal close_chadoxml (mimics original use by FlyBase).

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