def _get_ahringer_384_parent(child_stock):
"""
Get the 384-format LibraryStock corresponding to a 96-format child stock.
Assumes standard Ahringer naming conventions.
If the parent doesn't exist, creates it, assuming same parent
as the child.
"""
child_plate_parts = child_stock.plate.id.split('-')
parent_plate_name = child_plate_parts[0] + '-' + child_plate_parts[1]
parent_plate = get_library_plate(parent_plate_name)
child_well = child_stock.well
parent_well = get_384_parent_well(child_plate_parts[2], child_well)
parent_pk = generate_library_stock_name(parent_plate_name, parent_well)
try:
parent_stock = LibraryStock.objects.get(pk=parent_pk)
except ObjectDoesNotExist:
parent_stock = LibraryStock(
id=parent_pk,
plate=parent_plate,
well=parent_well,
parent_stock=None,
intended_clone=child_stock.intended_clone,
)
parent_stock.save()
return parent_stock
def _get_ahringer_384_parent(child_stock):
"""
Get the 384-format LibraryStock corresponding to a 96-format child stock.
Assumes standard Ahringer naming conventions.
If the parent doesn't exist, creates it, assuming same parent
as the child.
"""
child_plate_parts = child_stock.plate.id.split('-')
parent_plate_name = child_plate_parts[0] + '-' + child_plate_parts[1]
parent_plate = get_library_plate(parent_plate_name)
child_well = child_stock.well
parent_well = get_384_parent_well(child_plate_parts[2], child_well)
parent_pk = generate_library_stock_name(parent_plate_name, parent_well)
try:
parent_stock = LibraryStock.objects.get(pk=parent_pk)
except ObjectDoesNotExist:
parent_stock = LibraryStock(
id=parent_pk,
plate=parent_plate,
well=parent_well,
parent_stock=None,
intended_clone=child_stock.intended_clone,
)
parent_stock.save()
return parent_stock
def handle(self, **options):
require_db_write_acknowledgement()
all_wells = get_well_set()
# Get all wells, to determine which wells are missing.
#
# Skip 384-well plates, since the empty wells from these Ahringer
# parent plates can be created in concert with their 96-well children.
#
# Also skip 'GHR-' style plates. Since we don't actually have these
# plates in the lab, we only care about the small fraction of the
# wells from these plates that were used to generated our Vidal
# rearrays.
library_stocks = (LibraryStock.objects.filter(
plate__number_of_wells=96).exclude(plate__id__startswith='GHR-'))
plate_wells = {}
for library_stock in library_stocks:
if library_stock.plate not in plate_wells:
plate_wells[library_stock.plate] = set()
plate_wells[library_stock.plate].add(library_stock.well)
for library_plate in plate_wells:
missing_wells = all_wells - plate_wells[library_plate]
for missing_well in missing_wells:
library_stock = LibraryStock(
id=generate_library_stock_name(library_plate.id,
missing_well),
plate=library_plate,
well=missing_well,
parent_stock=None,
intended_clone=None,
)
if library_plate.is_ahringer_96_plate():
parent_stock = _get_ahringer_384_parent(library_stock)
if parent_stock.intended_clone:
self.stderr.write(
'384 well {} has a non-null intended clone, '
'but its 96-well derivative {} is empty\n'.format(
parent_stock, library_stock))
library_stock.parent_stock = parent_stock
library_stock.save()
def handle(self, **options):
require_db_write_acknowledgement()
all_wells = get_well_set()
# Get all wells, to determine which wells are missing.
#
# Skip 384-well plates, since the empty wells from these Ahringer
# parent plates can be created in concert with their 96-well children.
#
# Also skip 'GHR-' style plates. Since we don't actually have these
# plates in the lab, we only care about the small fraction of the
# wells from these plates that were used to generated our Vidal
# rearrays.
library_stocks = (LibraryStock.objects
.filter(plate__number_of_wells=96)
.exclude(plate__id__startswith='GHR-'))
plate_wells = {}
for library_stock in library_stocks:
if library_stock.plate not in plate_wells:
plate_wells[library_stock.plate] = set()
plate_wells[library_stock.plate].add(library_stock.well)
for library_plate in plate_wells:
missing_wells = all_wells - plate_wells[library_plate]
for missing_well in missing_wells:
library_stock = LibraryStock(
id=generate_library_stock_name(library_plate.id,
missing_well),
plate=library_plate, well=missing_well,
parent_stock=None, intended_clone=None,
)
if library_plate.is_ahringer_96_plate():
parent_stock = _get_ahringer_384_parent(library_stock)
if parent_stock.intended_clone:
self.stderr.write(
'384 well {} has a non-null intended clone, '
'but its 96-well derivative {} is empty\n'
.format(parent_stock, library_stock))
library_stock.parent_stock = parent_stock
library_stock.save()
