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://github.com/bioperl/bioperl-live/issues

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).