Package BioSQL :: Module BioSeqDatabase :: Class BioSeqDatabase

Class BioSeqDatabase

Represents a namespace (sub-database) within the BioSQL database.

i.e. One row in the biodatabase table, and all all rows in the bioentry
table associated with it.

Instance Methods

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__init__(self, adaptor, name)

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__repr__(self)

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get_Seq_by_id(self, name)
Gets a DBSeqRecord object by its name

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get_Seq_by_acc(self, name)
Gets a DBSeqRecord object by accession number

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get_Seq_by_ver(self, name)
Gets a DBSeqRecord object by version number

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get_Seqs_by_acc(self, name)
Gets a list of DBSeqRecord objects by accession number

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get_all_primary_ids(self)
All the primary_ids of the sequences in the database (OBSOLETE).

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__getitem__(self, key)

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__delitem__(self, key)
Remove an entry and all its annotation.

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__len__(self)
Number of records in this namespace (sub database).

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__contains__(self, value)
Check if a primary (internal) id is this namespace (sub database).

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__iter__(self)
Iterate over ids (which may not be meaningful outside this database).

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iterkeys(self)
Iterate over ids (which may not be meaningful outside this database).

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itervalues(self)
Iterate over DBSeqRecord objects in the namespace (sub database).

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iteritems(self)
Iterate over (id, DBSeqRecord) for the namespace (sub database).

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keys(self)
List of ids which may not be meaningful outside this database.

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values(self)
List of DBSeqRecord objects in the namespace (sub database).

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items(self)
List of (id, DBSeqRecord) for the namespace (sub database).

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lookup(self, **kwargs)

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get_Seq_by_primary_id(self, seqid)
Get a DBSeqRecord by the primary (internal) id (OBSOLETE).

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load(self, record_iterator, fetch_NCBI_taxonomy=False)
Load a set of SeqRecords into the BioSQL database.

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Method Details

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get_Seq_by_id(self, name)

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Gets a DBSeqRecord object by its name

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

The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.

get_Seq_by_acc(self, name)

source code

Gets a DBSeqRecord object by accession number

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

The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.

get_Seq_by_ver(self, name)

source code

Gets a DBSeqRecord object by version number

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

The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.

get_Seqs_by_acc(self, name)

source code

Gets a list of DBSeqRecord objects by accession number

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

The name of this method is misleading since it returns a list of
DBSeqRecord objects rather than a list of DBSeq ojbects, and presumably
was to mirror BioPerl.

get_all_primary_ids(self)

source code

All the primary_ids of the sequences in the database (OBSOLETE).

These maybe ids (display style) or accession numbers or
something else completely different - they *are not*
meaningful outside of this database implementation.

Please use .keys() instead of .get_all_primary_ids()

get_Seq_by_primary_id(self, seqid)

source code

Get a DBSeqRecord by the primary (internal) id (OBSOLETE).

Rather than db.get_Seq_by_primary_id(my_id) use db[my_id]

The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.

load(self, record_iterator, fetch_NCBI_taxonomy=False)

source code

Load a set of SeqRecords into the BioSQL database.

record_iterator is either a list of SeqRecord objects, or an
Iterator object that returns SeqRecord objects (such as the
output from the Bio.SeqIO.parse() function), which will be
used to populate the database.

fetch_NCBI_taxonomy is boolean flag allowing or preventing
connection to the taxonomic database on the NCBI server
(via Bio.Entrez) to fetch a detailed taxonomy for each
SeqRecord.

Example:
from Bio import SeqIO
count = db.load(SeqIO.parse(open(filename), format))

Returns the number of records loaded.