Package Bio :: Package SeqIO :: Module SeqXmlIO :: Class SeqXmlWriter

Class SeqXmlWriter

                     object --+        
                              |        
      Interfaces.SequenceWriter --+    
                                  |    
Interfaces.SequentialSequenceWriter --+
                                      |
                                     SeqXmlWriter

Writes SeqRecords into seqXML file.

SeqXML requires the sequence alphabet be explicitly RNA, DNA or protein, i.e. an instance or subclass of Bio.Alphapet.RNAAlphabet, Bio.Alphapet.DNAAlphabet or Bio.Alphapet.ProteinAlphabet.

Instance Methods

[hide private]

__init__(self, handle, source=None, source_version=None, species=None, ncbiTaxId=None)
Create Object and start the xml generator.

source code

write_header(self)
Write root node with document metadata.

source code

write_record(self, record)
Write one record.

source code

write_footer(self)
Close the root node and finish the XML document.

source code

_write_species(self, record)
Write the species if given.

source code

_write_description(self, record)
Write the description if given.

source code

_write_seq(self, record)
Write the sequence.

source code

_write_dbxrefs(self, record)
Write all database cross references.

source code

_write_properties(self, record)
Write all annotations that are key value pairs with values of a primitive type or list of primitive types.

source code

Inherited from Interfaces.SequentialSequenceWriter: write_file, write_records

Inherited from Interfaces.SequenceWriter: clean

Inherited from Interfaces.SequenceWriter (private): _get_seq_string

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__