Reference

Bio::SeqIO::flybase_chadoxml(3pm)

FlyBase variant of chadoxml with sequence output stream

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

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).

History