Method Summary |
|
__init__ (self,
adaptor,
dbid)
Initialize with connection information for the database. |
|
load_seqrecord (self,
record)
Load a Biopython SeqRecord into the database. |
|
_add_dbxref (self,
dbname,
accession,
version)
Insert a dbxref and return its id |
|
_get_ontology_id(self,
name,
definition)
|
|
_get_taxon_id (self,
record)
Get the id corresponding to a taxon. |
|
_get_term_id (self,
name,
ontology_id,
definition,
identifier)
Get the id that corresponds to a term. |
|
_insert_seqfeature_location (self,
feature,
rank,
seqfeature_id)
Add a location of a SeqFeature to the seqfeature_location table. |
|
_load_bioentry_date (self,
record,
bioentry_id)
Add the effective date of the entry into the database. |
|
_load_bioentry_table (self,
record)
Fill the bioentry table with sequence information. |
|
_load_biosequence (self,
record,
bioentry_id)
Load the biosequence table in the database. |
|
_load_comment(self,
record,
bioentry_id)
|
|
_load_reference(self,
reference,
rank,
bioentry_id)
|
|
_load_seqfeature (self,
feature,
feature_rank,
bioentry_id)
Load a biopython SeqFeature into the database. |
|
_load_seqfeature_basic (self,
feature_type,
feature_rank,
bioentry_id)
Load the first tables of a seqfeature and returns the id. |
|
_load_seqfeature_locations (self,
feature,
seqfeature_id)
Load all of the locations for a SeqFeature into tables. |
|
_load_seqfeature_qualifiers (self,
qualifiers,
seqfeature_id)
Insert the (key, value) pair qualifiers relating to a feature. |
_load_seqfeature_locations(self,
feature,
seqfeature_id)
Load all of the locations for a SeqFeature into tables.
This adds the locations related to the SeqFeature into the
seqfeature_location table. Fuzzies are not handled right now.
For a simple location, ie (1..2), we have a single table row
with seq_start = 1, seq_end = 2, location_rank = 1.
For split locations, ie (1..2, 3..4, 5..6) we would have three
row tables with:
start = 1, end = 2, rank = 1
start = 3, end = 4, rank = 2
start = 5, end = 6, rank = 3
-
|