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


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


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
    #after writing all seqs


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


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AUTHOR - Peili Zhang



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


 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   :


 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   :


 Title   : write_seq
 Usage   : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype,
                  -nounflatten=>0 or 1,
                  -is_analysis=>'true' or 'false',
 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).

2018-10-27 perl v5.26.2