def get_optimem_dilution_factor_from_molecule_type(cls, molecule_type):
"""
Returns the optimem dilution factor for a molecule type or molecule
type name.
:param molecule_type: The molecule types for the molecule design pool.
:type molecule_type: :class:`thelma.entities.moleculetype.MoleculeType`
or :class:`str` (molecule type ID)
:raises TypeError: For molecule types of the wrong class.
:raises ValueError: If the molecule type is unknown.
:return: The OptiMem dilution factor for this molecule type.
"""
if isinstance(molecule_type, MoleculeType):
mt_id = molecule_type.id
elif isinstance(molecule_type, basestring):
if MOLECULE_TYPE_IDS.is_known_type(molecule_type):
mt_id = molecule_type
else:
msg = 'Unknown molecule type name "%s".' % (molecule_type)
raise ValueError(msg)
else:
msg = 'The molecule types must be a %s object or a string ' \
'(obtained: %s).' % (MoleculeType.__class__.__name__,
molecule_type.__class__.__name__)
raise TypeError(msg)
if mt_id == MOLECULE_TYPE_IDS.MIRNA_INHI or \
mt_id == MOLECULE_TYPE_IDS.MIRNA_MIMI:
return cls.MIRNA_OPTIMEM_DILUTION_FACTOR
else:
return cls.STANDARD_OPTIMEM_DILUTION_FACTOR
def get_optimem_dilution_factor_from_molecule_type(cls, molecule_type):
"""
Returns the optimem dilution factor for a molecule type or molecule
type name.
:param molecule_type: The molecule types for the molecule design pool.
:type molecule_type: :class:`thelma.entities.moleculetype.MoleculeType`
or :class:`str` (molecule type ID)
:raises TypeError: For molecule types of the wrong class.
:raises ValueError: If the molecule type is unknown.
:return: The OptiMem dilution factor for this molecule type.
"""
if isinstance(molecule_type, MoleculeType):
mt_id = molecule_type.id
elif isinstance(molecule_type, basestring):
if MOLECULE_TYPE_IDS.is_known_type(molecule_type):
mt_id = molecule_type
else:
msg = 'Unknown molecule type name "%s".' % (molecule_type)
raise ValueError(msg)
else:
msg = 'The molecule types must be a %s object or a string ' \
'(obtained: %s).' % (MoleculeType.__class__.__name__,
molecule_type.__class__.__name__)
raise TypeError(msg)
if mt_id == MOLECULE_TYPE_IDS.MIRNA_INHI or \
mt_id == MOLECULE_TYPE_IDS.MIRNA_MIMI:
return cls.MIRNA_OPTIMEM_DILUTION_FACTOR
else:
return cls.STANDARD_OPTIMEM_DILUTION_FACTOR
def from_molecule_type(cls, molecule_type, number_designs=1):
"""
Returns the stock concentration for the given molecule type.
:param molecule_type: The molecule types whose stock concentration
you want to know.
:type molecule_type: :class:`thelma.entities.moleculetype.MoleculeType`
or :class:`str` (molecule type ID)
:param number_designs: The number of designs in a pool (at the moment
this is only makes a difference for siRNA pools).
:type number_designs: positive integer
:default number_designs: 1
:raises TypeError: For molecule types of the wrong class.
:raises ValueError: If the molecule type is unknown.
:return: The stock concentration for that molecule type in nM.
"""
if isinstance(molecule_type, MoleculeType):
mt_id = molecule_type.id
elif isinstance(molecule_type, basestring):
if MOLECULE_TYPE_IDS.is_known_type(molecule_type):
mt_id = molecule_type
else:
msg = 'Unknown molecule type name "%s".' % (molecule_type)
raise ValueError(msg)
else:
msg = 'The molecule types must be a %s object or a string ' \
'(obtained: %s).' % (MoleculeType.__class__.__name__,
molecule_type.__class__.__name__)
raise TypeError(msg)
if mt_id == MOLECULE_TYPE_IDS.MIRNA_INHI or \
mt_id == MOLECULE_TYPE_IDS.MIRNA_MIMI:
return cls._MICRO_RNA_STOCK_CONCENTRATION
elif mt_id == MOLECULE_TYPE_IDS.ESI_RNA:
return cls._ESI_RNA_STOCK_CONCENTRATION
elif mt_id == MOLECULE_TYPE_IDS.COMPOUND:
return cls.COMPOUND_STOCK_CONCENTRATION
elif mt_id == MOLECULE_TYPE_IDS.SIRNA and number_designs > 1:
return cls._SIRNA_POOL_CONCENTRATION
else:
return cls._STANDARD_STOCK_CONCENTRATION
