Package BioSQL :: Module BioSeq :: Class DBSeqRecord
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Class DBSeqRecord

source code

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: __len__, __nonzero__, __repr__, __str__

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

__init__(self, adaptor, primary_id)
(Constructor)

source code 

Create a SeqRecord.

Arguments: seq - Sequence, required (Seq object) 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)

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.

You can create a 'blank' SeqRecord object, and then populated the attributes later. Note that currently the annotations dictionary cannot be specified when creating the SeqRecord.

Overrides: Bio.SeqRecord.SeqRecord.__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)