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

Module BioSeq

source code

Implementations of Biopython-like Seq objects on top of BioSQL.

This allows retrival of items stored in a BioSQL database using
a biopython-like SeqRecord and Seq interface.

Note: Currently we do not support recording per-letter-annotations
(like quality scores) in BioSQL.

Classes [hide private]
  DBSeq
BioSQL equivalent of the Biopython Seq object.
  DBSeqRecord
BioSQL equivalent of the Biopython SeqRecord object.
Functions [hide private]
 
_retrieve_seq(adaptor, primary_id) source code
 
_retrieve_dbxrefs(adaptor, primary_id)
Retrieve the database cross references for the sequence.
source code
 
_retrieve_features(adaptor, primary_id) source code
 
_retrieve_location_qualifier_value(adaptor, location_id) source code
 
_retrieve_annotations(adaptor, primary_id, taxon_id) source code
 
_make_unicode_into_string(text) source code
 
_retrieve_qualifier_value(adaptor, primary_id) source code
 
_retrieve_reference(adaptor, primary_id) source code
 
_retrieve_taxon(adaptor, primary_id, taxon_id) source code
 
_retrieve_comment(adaptor, primary_id) source code
Variables [hide private]
  __package__ = 'BioSQL'