def __init__(self, adaptor, primary_id):
"""Create a DBSeqRecord object.
Arguments:
- adaptor - A BioSQL.BioSeqDatabase.Adaptor object
- primary_id - An internal integer ID used by BioSQL
You wouldn't normally create a DBSeqRecord object yourself,
this is done for you when using a BioSeqDatabase object
"""
self._adaptor = adaptor
self._primary_id = primary_id
(self._biodatabase_id, self._taxon_id, self.name,
accession, version, self._identifier,
self._division, self.description) = self._adaptor.execute_one(
"SELECT biodatabase_id, taxon_id, name, accession, version,"
" identifier, division, description"
" FROM bioentry"
" WHERE bioentry_id = %s", (self._primary_id,))
if version and version != "0":
self.id = "%s.%s" % (accession, version)
else:
self.id = accession
# We don't yet record any per-letter-annotations in the
# BioSQL database, but we should set this property up
# for completeness (and the __str__ method).
# We do NOT want to load the sequence from the DB here!
length = _retrieve_seq_len(adaptor, primary_id)
self._per_letter_annotations = _RestrictedDict(length=length)
def __init__(self, adaptor, primary_id):
"""Create a DBSeqRecord object.
Arguments:
- adaptor - A BioSQL.BioSeqDatabase.Adaptor object
- primary_id - An internal integer ID used by BioSQL
You wouldn't normally create a DBSeqRecord object yourself,
this is done for you when using a BioSeqDatabase object
"""
self._adaptor = adaptor
self._primary_id = primary_id
(self._biodatabase_id, self._taxon_id, self.name,
accession, version, self._identifier,
self._division, self.description) = self._adaptor.execute_one(
"SELECT biodatabase_id, taxon_id, name, accession, version,"
" identifier, division, description"
" FROM bioentry"
" WHERE bioentry_id = %s", (self._primary_id,))
if version and version != "0":
self.id = "%s.%s" % (accession, version)
else:
self.id = accession
# We don't yet record any per-letter-annotations in the
# BioSQL database, but we should set this property up
# for completeness (and the __str__ method).
# We do NOT want to load the sequence from the DB here!
length = _retrieve_seq_len(adaptor, primary_id)
self._per_letter_annotations = _RestrictedDict(length=length)
def _get_per_column_annotations(self):
if self._per_col_annotations is None:
# This happens if empty at initialisation
if len(self):
# Use the standard method to get the length
expected_length = self.get_alignment_length()
else:
# Should this raise an exception? Compare SeqRecord behaviour...
expected_length = 0
self._per_col_annotations = _RestrictedDict(length=expected_length)
return self._per_col_annotations
def _get_per_column_annotations(self):
if self._per_col_annotations is None:
# This happens if empty at initialisation
if len(self):
# Use the standard method to get the length
expected_length = self.get_alignment_length()
else:
# Should this raise an exception? Compare SeqRecord behaviour...
expected_length = 0
self._per_col_annotations = _RestrictedDict(length=expected_length)
return self._per_col_annotations
def _set_per_column_annotations(self, value):
if not isinstance(value, dict):
raise TypeError("The per-column-annotations should be a "
"(restricted) dictionary.")
# Turn this into a restricted-dictionary (and check the entries)
if len(self):
# Use the standard method to get the length
expected_length = self.get_alignment_length()
self._per_col_annotations = _RestrictedDict(length=expected_length)
self._per_col_annotations.update(value)
else:
# Bit of a problem case... number of columns is undefined
self._per_col_annotations = None
if value:
raise ValueError("Can't set per-column-annotations without an alignment")
def _set_per_column_annotations(self, value):
if not isinstance(value, dict):
raise TypeError("The per-column-annotations should be a "
"(restricted) dictionary.")
# Turn this into a restricted-dictionary (and check the entries)
if len(self):
# Use the standard method to get the length
expected_length = self.get_alignment_length()
self._per_col_annotations = _RestrictedDict(length=expected_length)
self._per_col_annotations.update(value)
else:
# Bit of a problem case... number of columns is undefined
self._per_col_annotations = None
if value:
raise ValueError("Can't set per-column-annotations without an alignment")
def __init__(self, adaptor, primary_id):
self._adaptor = adaptor
self._primary_id = primary_id
(self._biodatabase_id, self._taxon_id, self.name, accession, version,
self._identifier, self._division,
self.description) = self._adaptor.execute_one(
"SELECT biodatabase_id, taxon_id, name, accession, version,"
" identifier, division, description"
" FROM bioentry"
" WHERE bioentry_id = %s", (self._primary_id, ))
if version and version != "0":
self.id = "%s.%s" % (accession, version)
else:
self.id = accession
# We don't yet record any per-letter-annotations in the
# BioSQL database, but we should set this property up
# for completeness (and the __str__ method).
# We do NOT want to load the sequence from the DB here!
length = _retrieve_seq_len(adaptor, primary_id)
self._per_letter_annotations = _RestrictedDict(length=length)
def __init__(self, adaptor, primary_id):
self._adaptor = adaptor
self._primary_id = primary_id
(self._biodatabase_id, self._taxon_id, self.name,
accession, version, self._identifier,
self._division, self.description) = self._adaptor.execute_one(
"SELECT biodatabase_id, taxon_id, name, accession, version,"
" identifier, division, description"
" FROM bioentry"
" WHERE bioentry_id = %s", (self._primary_id,))
if version and version != "0":
self.id = "%s.%s" % (accession, version)
else:
self.id = accession
# We don't yet record any per-letter-annotations in the
# BioSQL database, but we should set this property up
# for completeness (and the __str__ method).
# We do NOT want to load the sequence from the DB here!
length = _retrieve_seq_len(adaptor, primary_id)
self._per_letter_annotations = _RestrictedDict(length=length)
def __init__(self, adaptor, primary_id):
self._adaptor = adaptor
self._primary_id = primary_id
(self._biodatabase_id, self._taxon_id, self.name,
accession, version, self._identifier,
self._division, self.description) = self._adaptor.execute_one(
"SELECT biodatabase_id, taxon_id, name, accession, version," \
" identifier, division, description" \
" FROM bioentry" \
" WHERE bioentry_id = %s", (self._primary_id,))
if version and version != "0":
self.id = "%s.%s" % (accession, version)
else:
self.id = accession
#We don't yet record any per-letter-annotations in the
#BioSQL database, but we should set this property up
#for completeness (and the __str__ method).
try :
length = len(self.seq)
except :
#Could be no sequence in the database!
length = 0
self._per_letter_annotations = _RestrictedDict(length=length)
def __init__(self, adaptor, primary_id):
self._adaptor = adaptor
self._primary_id = primary_id
(self._biodatabase_id, self._taxon_id, self.name,
accession, version, self._identifier,
self._division, self.description) = self._adaptor.execute_one(
"SELECT biodatabase_id, taxon_id, name, accession, version," \
" identifier, division, description" \
" FROM bioentry" \
" WHERE bioentry_id = %s", (self._primary_id,))
if version and version != "0":
self.id = "%s.%s" % (accession, version)
else:
self.id = accession
#We don't yet record any per-letter-annotations in the
#BioSQL database, but we should set this property up
#for completeness (and the __str__ method).
try:
length = len(self.seq)
except:
#Could be no sequence in the database!
length = 0
self._per_letter_annotations = _RestrictedDict(length=length)
