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 get_library_stock(legacy_plate_name, well):
"""Get a library well from its legacy plate name and well."""
library_stock_name = generate_library_stock_name(legacy_plate_name, well)
try:
return LibraryStock.objects.get(id=library_stock_name)
except ObjectDoesNotExist:
raise ObjectDoesNotExist(get_missing_object_message(
'LibraryStock', id=library_stock_name))
def sync_secondary_L4440_row(legacy_row):
plate_name = legacy_row[0]
well = get_three_character_well(legacy_row[1])
new_well = LibraryStock(
id=generate_library_stock_name(plate_name, well),
plate=get_library_plate(plate_name), well=well,
parent_stock=None, intended_clone=get_clone('L4440'))
return update_or_save_object(command, new_well, recorded_wells,
fields_to_compare)
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()
def sync_primary_row(legacy_row):
plate_name = legacy_row[0]
well = get_three_character_well(legacy_row[1])
clone_name = legacy_row[2]
parent_plate_name = legacy_row[4]
if re.match('sjj', clone_name):
parent_chromosome = legacy_row[3]
parent_plate_name = generate_ahringer_384_plate_name(
parent_chromosome, parent_plate_name)
parent_well_improper = legacy_row[5]
if re.match('mv', clone_name):
clone_name = generate_vidal_clone_name(parent_plate_name,
parent_well_improper)
intended_clone = get_clone(clone_name)
if re.match('L4440', clone_name):
parent_stock = None
else:
parent_well_proper = get_three_character_well(parent_well_improper)
parent_stock = get_library_stock(parent_plate_name,
parent_well_proper)
# Confirm that this intended clone matches parent's clone
if parent_stock.intended_clone != intended_clone:
raise CommandError('Clone {} does not match parent\n'
.format(clone_name))
new_well = LibraryStock(
id=generate_library_stock_name(plate_name, well),
plate=get_library_plate(plate_name), well=well,
parent_stock=parent_stock,
intended_clone=intended_clone)
return update_or_save_object(command, new_well, recorded_wells,
fields_to_compare)
def sync_source_row(legacy_row):
plate_name = legacy_row[0]
clone_name = legacy_row[3]
if re.match('sjj', clone_name):
chromosome = legacy_row[2]
plate_name = generate_ahringer_384_plate_name(
chromosome, plate_name)
well_improper = legacy_row[1]
well_proper = get_three_character_well(well_improper)
if re.match('mv', clone_name):
clone_name = generate_vidal_clone_name(plate_name,
well_improper)
new_well = LibraryStock(
id=generate_library_stock_name(plate_name, well_proper),
plate=get_library_plate(plate_name), well=well_proper,
parent_stock=None, intended_clone=get_clone(clone_name))
return update_or_save_object(command, new_well, recorded_wells,
fields_to_compare)
def sync_eliana_row(legacy_row):
plate_name = legacy_row[0]
well = get_three_character_well(legacy_row[1])
if legacy_row[2]:
try:
parent_stock = get_library_stock(legacy_row[2], legacy_row[3])
intended_clone = parent_stock.intended_clone
except ObjectDoesNotExist:
parent_stock = None
intended_clone = None
else:
parent_stock = None
intended_clone = None
new_well = LibraryStock(
id=generate_library_stock_name(plate_name, well),
plate=get_library_plate(plate_name), well=well,
parent_stock=parent_stock,
intended_clone=intended_clone)
return update_or_save_object(command, new_well, recorded_wells,
fields_to_compare)
def sync_secondary_row(legacy_row):
plate_name = legacy_row[0]
well = get_three_character_well(legacy_row[1])
clone_name = legacy_row[2]
definite_parent_plate_name = legacy_row[3]
definite_parent_well = legacy_row[4]
if definite_parent_well:
definite_parent_well = get_three_character_well(
definite_parent_well)
likely_parent_plate_name = legacy_row[5]
likely_parent_well = legacy_row[6]
if likely_parent_well:
likely_parent_well = get_three_character_well(likely_parent_well)
likely_parent_clone_name = legacy_row[7]
if (definite_parent_plate_name and likely_parent_plate_name and
definite_parent_plate_name != likely_parent_plate_name):
raise CommandError(
'ERROR: definite and likely parent plates disagree '
'for {} {}\n'.format(plate_name, well))
if (definite_parent_well and likely_parent_well and
definite_parent_well != likely_parent_well):
raise CommandError(
'ERROR: definite and likely parent wells disagree '
'for {} {}\n'.format(plate_name, well))
try:
if definite_parent_plate_name and definite_parent_well:
parent_stock = get_library_stock(definite_parent_plate_name,
definite_parent_well)
else:
parent_stock = get_library_stock(likely_parent_plate_name,
likely_parent_well)
intended_clone = parent_stock.intended_clone
except ObjectDoesNotExist:
command.stderr.write(
'WARNING for LibraryStock {} {}: parent not '
'found in LibraryStock\n'.format(plate_name, well))
parent_stock = None
intended_clone = None
if clone_name and (clone_name != likely_parent_clone_name):
command.stderr.write(
'WARNING for LibraryStock {} {}: clone recorded '
'in CherryPickRNAiPlate is inconsistent with '
'CherryPickTemplate source/destination records\n'
.format(plate_name, well))
if re.match('sjj', clone_name):
try:
recorded_clone = get_clone(clone_name)
if recorded_clone != intended_clone:
command.stderr.write(
'WARNING for LibraryStock {} {}: clone recorded '
'in CherryPickRNAiPlate does not match its '
'parent\'s clone\n'.format(plate_name, well))
except ObjectDoesNotExist:
command.stderr.write(
'WARNING for LibraryStock {} {}: clone recorded in '
'CherryPickRNAiPlate not found at all in RNAiPlate\n'
.format(plate_name, well))
new_well = LibraryStock(
id=generate_library_stock_name(plate_name, well),
plate=get_library_plate(plate_name), well=well,
parent_stock=parent_stock,
intended_clone=intended_clone)
return update_or_save_object(command, new_well, recorded_wells,
fields_to_compare)