def handle(self, **options):
positives = get_positives_any_worm('SUP', 2, criteria)
seqs = (LibrarySequencing.objects
.filter(source_stock__in=positives)
.select_related('source_stock',
'source_stock__intended_clone'))
categorized_seqs = categorize_sequences_by_blat_results(seqs)
stocks_to_resequence = []
for category, values in categorized_seqs.items():
if _should_be_redone(category):
stocks_to_resequence.extend(
[x.source_stock for x in values])
stocks_to_resequence = sorted(stocks_to_resequence,
key=lambda stock: stock.id)
assigned = assign_to_plates(
stocks_to_resequence, vertical=True,
empties_per_plate=options['empties_per_plate'])
rows = get_plate_assignment_rows(assigned)
# Write output
self.stdout.write('source_plate,source_well,'
'destination_plate,destination_well')
for row in rows:
destination_plate = get_destination_plate(
row[0], options['first_plate_number'])
destination_well = row[1]
source = row[2]
if hasattr(source, 'plate'):
source_plate = source.plate
else:
source_plate = None
if hasattr(source, 'well'):
source_well = source.well
else:
source_well = None
self.stdout.write('{},{},{},{}'.format(
source_plate, source_well,
destination_plate, destination_well))
def handle(self, **options):
summary_mode = options['summary']
candidates_by_worm = {}
candidates_by_clone = {}
worms = WormStrain.get_worms_for_screen_type('ENH')
for worm in worms:
candidates_by_worm[worm] = []
singles = worm.get_stocks_tested_by_number_of_replicates(
'ENH', 1, 1)
positives = worm.get_positives('ENH',
1,
passes_enh_primary,
singles=singles)
for library_stock in positives:
candidates_by_worm[worm].append(library_stock)
if library_stock not in candidates_by_clone:
candidates_by_clone[library_stock] = []
candidates_by_clone[library_stock].append(worm)
if summary_mode:
self.stdout.write('Total clones to cherrypick: {}'.format(
len(candidates_by_clone)))
self.stdout.write('\n\nBefore accounting for universals:')
_print_candidates_by_worm(candidates_by_worm)
# Move certain clones from individual worm lists to universal
candidates_by_worm['universal'] = []
for well in candidates_by_clone:
worms = (candidates_by_clone[well])
if len(worms) >= UNIVERSAL_THRESHOLD:
candidates_by_worm['universal'].append(well)
for worm in worms:
candidates_by_worm[worm].remove(well)
if summary_mode:
self.stdout.write('\n\nAfter accounting for universals:')
_print_candidates_by_worm(candidates_by_worm)
return
# Create official cherrypick list, with random empty wells
cherrypick_list = []
already_used_empties = set()
for worm, candidates in candidates_by_worm.iteritems():
label = worm.allele if hasattr(worm, 'allele') else worm
if label == 'universal':
empties_per_plate = 1
empties_limit = 9
elif label == 'it57':
empties_per_plate = 0
empties_limit = None
else:
empties_per_plate = 2
empties_limit = None
assigned = assign_to_plates(
sorted(candidates),
vertical=True,
empties_per_plate=empties_per_plate,
empties_limit=empties_limit,
already_used_empties=already_used_empties)
rows = get_plate_assignment_rows(assigned)
for row in rows:
if row[2]:
source_plate = row[2].plate
source_well = row[2].well
else: # Empty well
source_plate = None
source_well = None
destination_plate = label + '-E' + str(row[0] + 1)
destination_well = row[1]
cherrypick_list.append((source_plate, source_well,
destination_plate, destination_well))
# Sort by (destination_plate, destination_well)
cherrypick_list.sort(key=lambda x: (x[2].split('-')[
0], int(x[2].split('E')[1]), int(x[3][1:]), x[3][0]))
# Print the list
self.stdout.write('source_plate,source_well,'
'destination_plate,destination_well')
for row in cherrypick_list:
self.stdout.write(','.join([str(x) for x in row]))
# Quick fix for empty_wells check up to this point not accounting
# for not-full plates potentially having the same plate pattern,
# despite the "chosen" empty wells differing.
# If the printed list says "TRASH THIS" at the bottom, try again!
e = {}
for row in cherrypick_list:
if row[0] is None:
if row[2] not in e:
e[row[2]] = set()
e[row[2]].add(row[3])
seen = set()
for plate, wells in e.iteritems():
wells = tuple(sorted(wells))
if is_symmetric(wells):
self.stdout.write('TRASH THIS AND TRY AGAIN. '
'{}:{} pattern is symmetric!'.format(
plate, wells))
if wells in seen:
self.stdout.write('TRASH THIS AND TRY AGAIN. '
'{}:{} pattern redundant!'.format(
plate, wells))
seen.add(wells)