- AUTHOR - Peili Zhang
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 $writer->write_seq($seq_obj); #after writing all seqs $writer->close_chadoxml();
This is a simple subclass of Bio::SeqIO::chadoxml; please see its documentation for details.
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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=>$seqSOtype, -src_feature=>$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).