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 _
$obj->return_ftype_hash()
A simple hash where returning it has be factored out of the main code to allow subclasses to override it.
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.
The string that represents the SO term.
$obj->return_reltypename()
Return the appropriate relationship type name depending on the feature type (typically partof, but producedby for proteins).
A relationship type name.
A SO type name.
$obj->write_seq()
Overrides Bio::SeqIO::chadoxml's write_seq method just to add an internal close_chadoxml (mimics original use by FlyBase).
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.