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Package BioSQL :: Module BioSeqDatabase :: Class BioSeqDatabase |
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Method Summary | |
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__init__(self,
adaptor,
name)
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__getitem__(self,
key)
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__repr__(self)
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Array of all the primary_ids of the sequences in the database. | |
get_PrimarySeq_stream(self)
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Gets a Bio::Seq object by accession number | |
Gets a Bio::Seq object by its name | |
Gets a Bio::Seq object by the primary (internal) id. | |
Gets a Bio::Seq object by version number | |
Gets a *list* of Bio::Seq objects by accession number | |
items(self)
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keys(self)
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Load a set of SeqRecords into the BioSQL database. | |
lookup(self,
**kwargs)
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values(self)
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Method Details |
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get_all_primary_ids(self)Array of all the primary_ids of the sequences in the database. These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. |
get_Seq_by_acc(self, name)Gets a Bio::Seq object by accession number Example: seq = db.get_Seq_by_acc('X77802') |
get_Seq_by_id(self, name)Gets a Bio::Seq object by its name Example: seq = db.get_Seq_by_id('ROA1_HUMAN') |
get_Seq_by_primary_id(self, seqid)Gets a Bio::Seq object by the primary (internal) id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. |
get_Seq_by_ver(self, name)Gets a Bio::Seq object by version number Example: seq = db.get_Seq_by_ver('X77802.1') |
get_Seqs_by_acc(self, name)Gets a *list* of Bio::Seq objects by accession number Example: seqs = db.get_Seq_by_acc('X77802') |
load(self, record_iterator)Load a set of SeqRecords into the BioSQL database. record_iterator is an Iterator object that returns SeqRecord objects which will be used to populate the database. The Iterator should implement next() and either return None or raise StopIteration when it is out of objects. Returns the number of records loaded. |
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