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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
 
 

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:

   http://bugzilla.bioperl.org
 
 

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

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.

Arguments

The string that represents the SO term.

return_reltypename

Usage

   $obj->return_reltypename()
 
 

Function

Return the appropriate relationship type name depending on the feature type (typically partof, but producedby for proteins).

Returns

A relationship type name.

Arguments

A SO type name.

write_seq

Usage

   $obj->write_seq()
 
 

Function

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

Returns

Arguments