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

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

get_Seq_by_id(self, name)

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Gets a Bio::Seq object by its name

Example: seq = db.get_Seq_by_id('ROA1_HUMAN')

get_Seq_by_acc(self, name)

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Gets a Bio::Seq object by accession number

Example: seq = db.get_Seq_by_acc('X77802')

get_Seq_by_ver(self, name)

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Gets a Bio::Seq object by version number

Example: seq = db.get_Seq_by_ver('X77802.1')

get_Seqs_by_acc(self, name)

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Gets a *list* of Bio::Seq objects by accession number

Example: seqs = db.get_Seq_by_acc('X77802')

get_all_primary_ids(self)

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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_primary_id(self, seqid)

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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.

load(self, record_iterator)

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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.