Manual Reference Pages - BIO::SEQIO::FLYBASE_CHADOXML (3)
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.
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.
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::chadoxmls write_seq method just to add an internal
close_chadoxml (mimics original use by FlyBase).
|perl v5.20.3 ||BIO::SEQIO::FLYBASE_CHADOXML (3) ||2016-04-05 |
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