Package BioSQL :: Module BioSeq :: Class DBSeqRecord
[hide private]
[frames] | no frames]

Class DBSeqRecord

source code

             object --+    
                      |    
Bio.SeqRecord.SeqRecord --+
                          |
                         DBSeqRecord

BioSQL equivalent of the Biopython SeqRecord object.

Instance Methods [hide private]
 
__init__(self, adaptor, primary_id)
Create a SeqRecord.
source code
 
__get_seq(self) source code
 
__set_seq(self, seq) source code
 
__del_seq(self) source code
 
__get_dbxrefs(self) source code
 
__set_dbxrefs(self, dbxrefs) source code
 
__del_dbxrefs(self) source code
 
__get_features(self) source code
 
__set_features(self, features) source code
 
__del_features(self) source code
 
__get_annotations(self) source code
 
__set_annotations(self, annotations) source code
 
__del_annotations(self) source code

Inherited from Bio.SeqRecord.SeqRecord: __add__, __bool__, __contains__, __format__, __getitem__, __iter__, __len__, __nonzero__, __radd__, __repr__, __str__, format, lower, reverse_complement, upper

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

Properties [hide private]
  seq
Seq object
  dbxrefs
Database cross references
  features
Features
  annotations
Annotations

Inherited from Bio.SeqRecord.SeqRecord: letter_annotations

Inherited from object: __class__

Method Details [hide private]

__init__(self, adaptor, primary_id)
(Constructor)

source code 

Create a SeqRecord.

Arguments:
  • seq - Sequence, required (Seq, MutableSeq or UnknownSeq)

  • id - Sequence identifier, recommended (string)

  • name - Sequence name, optional (string)

  • description - Sequence description, optional (string)

  • dbxrefs - Database cross references, optional (list of strings)

  • features - Any (sub)features, optional (list of SeqFeature objects)

  • annotations - Dictionary of annotations for the whole sequence

  • letter_annotations - Dictionary of per-letter-annotations, values should be strings, list or tuples of the same length as the full sequence.

You will typically use Bio.SeqIO to read in sequences from files as SeqRecord objects. However, you may want to create your own SeqRecord objects directly.

Note that while an id is optional, we strongly recommend you supply a unique id string for each record. This is especially important if you wish to write your sequences to a file.

If you don't have the actual sequence, but you do know its length, then using the UnknownSeq object from Bio.Seq is appropriate.

You can create a 'blank' SeqRecord object, and then populate the attributes later.

Overrides: object.__init__
(inherited documentation)

Property Details [hide private]

seq

Seq object

Get Method:
__get_seq(self)
Set Method:
__set_seq(self, seq)
Delete Method:
__del_seq(self)

dbxrefs

Database cross references

Get Method:
__get_dbxrefs(self)
Set Method:
__set_dbxrefs(self, dbxrefs)
Delete Method:
__del_dbxrefs(self)

features

Features

Get Method:
__get_features(self)
Set Method:
__set_features(self, features)
Delete Method:
__del_features(self)

annotations

Annotations

Get Method:
__get_annotations(self)
Set Method:
__set_annotations(self, annotations)
Delete Method:
__del_annotations(self)