Package BioSQL :: Module BioSeq

Module BioSeq

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

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DBSeq

DBSeqRecord
BioSQL equivalent of the biopython SeqRecord object.

Functions

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_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)

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_retrieve_location_qualifier_value(adaptor, location_id)

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_retrieve_annotations(adaptor, primary_id, taxon_id)

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_make_unicode_into_string(text)

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_retrieve_qualifier_value(adaptor, primary_id)

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_retrieve_reference(adaptor, primary_id)

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_retrieve_taxon(adaptor, primary_id, taxon_id)

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_retrieve_comment(adaptor, primary_id)

source code