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)