Load a database with biopython objects.
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__init__(self,
adaptor,
dbid)
Initialize with connection information for the database. |
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load_seqrecord(self,
record)
Load a Biopython SeqRecord into the database. |
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_get_ontology_id(self,
name,
definition=None) |
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_get_term_id(self,
name,
ontology_id=None,
definition=None,
identifier=None)
Get the id that corresponds to a term. |
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_add_dbxref(self,
dbname,
accession,
version)
Insert a dbxref and return its id |
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_load_bioentry_table(self,
record)
Fill the bioentry table with sequence information. |
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_load_bioentry_date(self,
record,
bioentry_id)
Add the effective date of the entry into the database. |
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_load_biosequence(self,
record,
bioentry_id)
Load the biosequence table in the database. |
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_load_reference(self,
reference,
rank,
bioentry_id) |
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_load_seqfeature(self,
feature,
feature_rank,
bioentry_id)
Load a biopython SeqFeature into the database. |
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_insert_seqfeature_location(self,
feature,
rank,
seqfeature_id)
Add a location of a SeqFeature to the seqfeature_location table. |
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_get_dbxref_id(self,
db,
accession)
o db String, the name of the external database containing
the accession number |
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_get_seqfeature_dbxref(self,
seqfeature_id,
dbxref_id,
rank)
Check for a pre-existing seqfeature_dbxref entry with the passed
seqfeature_id and dbxref_id. |
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_add_seqfeature_dbxref(self,
seqfeature_id,
dbxref_id,
rank)
Insert a seqfeature_dbxref row and return the seqfeature_id and
dbxref_id |
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