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__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, handle, source=None, source_version=None, species=None, ncbiTaxId=None)
(Constructor)

source code

Create Object and start the xml generator.

Overrides: object.__init__

write_header(self)

source code

Write root node with document metadata.

Overrides: Interfaces.SequentialSequenceWriter.write_header

write_record(self, record)

source code

Write one record.

Overrides: Interfaces.SequentialSequenceWriter.write_record

write_footer(self)

source code

Close the root node and finish the XML document.

Overrides: Interfaces.SequentialSequenceWriter.write_footer

_write_seq(self, record)

source code

Write the sequence.

Note that SeqXML requires a DNA, RNA or protein alphabet.

Class SeqXmlWriter

__init__(self, handle, source=None, source_version=None, species=None, ncbiTaxId=None) (Constructor)

write_header(self)

write_record(self, record)

write_footer(self)

_write_seq(self, record)

init(self, handle, source=None, source_version=None, species=None, ncbiTaxId=None)
(Constructor)