Package BioSQL :: Module BioSeqDatabase :: Class BioSeqDatabase
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Class BioSeqDatabase


Method Summary
  __init__(self, adaptor, name)
  __getitem__(self, key)
  __repr__(self)
  get_all_primary_ids(self)
Array of all the primary_ids of the sequences in the database.
  get_PrimarySeq_stream(self)
  get_Seq_by_acc(self, name)
Gets a Bio::Seq object by accession number
  get_Seq_by_id(self, name)
Gets a Bio::Seq object by its name
  get_Seq_by_primary_id(self, seqid)
Gets a Bio::Seq object by the primary (internal) id.
  get_Seq_by_ver(self, name)
Gets a Bio::Seq object by version number
  get_Seqs_by_acc(self, name)
Gets a *list* of Bio::Seq objects by accession number
  items(self)
  keys(self)
  load(self, record_iterator)
Load a set of SeqRecords into the BioSQL database.
  lookup(self, **kwargs)
  values(self)

Method Details

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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