def test_get_worms_for_screen_type(self):
n2, dnc1, glp1, emb8 = self.get_worms()
enhs = WormStrain.get_worms_for_screen_type('ENH')
sups = WormStrain.get_worms_for_screen_type('SUP')
for worms in (enhs, sups):
self.assertNotIn(n2, worms)
self.assertIn(emb8, worms)
self.assertIn(dnc1, enhs)
self.assertNotIn(dnc1, sups)
self.assertNotIn(glp1, enhs)
self.assertIn(glp1, sups)
def get_n2_control_filters(self):
"""
Get the N2 + RNAi controls for this experiment.
It does this by manually setting the strain as N2 and then applying
all the other parameters which are shared by the controls.
To get the actual control experiments from the returned filters,
simply do Experiment.objects.filter(**filters). Returning
the filters is more flexible for customization, or for inserting
into a URL without performing the query.
N2 controls for this experiment are restricted to those from
the same date, *closest* temperature, same RNAi clone.
"""
filters = {
'is_junk': False,
'plate__date': self.date(),
'plate__temperature': self.temperature(),
'library_stock': self.library_stock,
'worm_strain': WormStrain.get_n2().pk,
}
filters['plate__temperature'] = Experiment.get_closest_temperature(
self.temperature(), filters)
return filters
def get_n2_l4440_control_filters(self):
"""
Get the filters for the L4440 controls for this experiment.
To get the actual control experiments from the returned filters,
simply do Experiment.objects.filter(**filters). Returning
the filters is more flexible for customization, or for inserting
into a URL without performing the query.
L4440 controls for this experiment are restricted to those from
the same date, same temperature, same worm.
If this experiment is itself an L4440 clone, the function works
the same way, returning all L4440 experiments from the same
date, same worm, same temperature.
"""
filters = {
'is_junk': False,
'plate__date': self.date(),
'plate__temperature': self.temperature(),
'worm_strain': WormStrain.get_n2().pk,
'library_stock__intended_clone': Clone.get_l4440(),
}
return filters
def clean_mutant_query_and_screen_type(form, cleaned_data):
"""
Helper to derive worm strain and temperature from cleaned_data.
If cleaned_data['mutant_query'] and cleaned_data['screen_type']
are defined, cleaned_data['worm'] and cleaned_data['temperature']
will be populated.
Returns the modified cleaned_data.
"""
mutant_query = cleaned_data.get('mutant_query')
secondary_mutant_query = cleaned_data.get('secondary_mutant_query')
screen_type = cleaned_data.get('screen_type')
if mutant_query and screen_type and secondary_mutant_query:
worm_and_temp = WormStrain.get_worm_and_temperature_from_search_term(
mutant_query, screen_type)
worm_and_temp2 = WormStrain.get_worm_and_temperature_from_search_term(
secondary_mutant_query, screen_type)
print worm_and_temp2
if worm_and_temp and worm_and_temp2:
cleaned_data['worm'] = worm_and_temp[0]
cleaned_data['worm2'] = worm_and_temp2[0]
cleaned_data['temperature'] = worm_and_temp[1]
else:
form.add_error('mutant_query', 'No mutant match')
elif mutant_query and screen_type:
worm_and_temp = WormStrain.get_worm_and_temperature_from_search_term(
mutant_query, screen_type)
if worm_and_temp:
cleaned_data['worm'] = worm_and_temp[0]
cleaned_data['worm2'] = secondary_mutant_query
cleaned_data['temperature'] = worm_and_temp[1]
else:
form.add_error('mutant_query', 'No mutant match')
return cleaned_data
def rnai_knockdown(request, clones, temperature=None):
"""
Render the page showing knockdown by RNAi only.
context['data'] is returned in format:
{clone: {
library_stock: [experiments]
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
filters = {
'is_junk': False,
'worm_strain': n2.pk,
'library_stock__intended_clone': clone,
}
if temperature:
filters['plate__temperature'] = temperature
# Do not join manual scores, since N2 not manually scored
experiments = (Experiment.objects.filter(**filters).select_related(
'library_stock',
'plate').prefetch_related('devstarscore_set').order_by(
'-library_stock__plate__screen_stage', 'library_stock',
'-plate__date', 'id'))
data_by_well = OrderedDict()
for experiment in experiments:
library_stock = experiment.library_stock
if library_stock not in data_by_well:
data_by_well[library_stock] = []
data_by_well[library_stock].append(experiment)
if data_by_well:
data[clone] = data_by_well
context = {
'n2': n2,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'rnai_knockdown.html', context)
def rnai_knockdown(request, clones, temperature=None):
"""
Render the page showing knockdown by RNAi only.
context['data'] is returned in format:
{clone: {
library_stock: [experiments]
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
filters = {
'is_junk': False,
'worm_strain': n2.pk,
'library_stock__intended_clone': clone,
}
if temperature:
filters['plate__temperature'] = temperature
# Do not join manual scores, since N2 not manually scored
experiments = (Experiment.objects.filter(**filters)
.select_related('library_stock', 'plate')
.prefetch_related('devstarscore_set')
.order_by('-library_stock__plate__screen_stage',
'library_stock', '-plate__date', 'id'))
data_by_well = OrderedDict()
for experiment in experiments:
library_stock = experiment.library_stock
if library_stock not in data_by_well:
data_by_well[library_stock] = []
data_by_well[library_stock].append(experiment)
if data_by_well:
data[clone] = data_by_well
context = {
'n2': n2,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'rnai_knockdown.html', context)
def get_positives_any_worm(screen_type, screen_stage, criteria, **kwargs):
"""
Get the set of library stocks that are positive for ANY worm.
A screen is defined by both screen_type ('ENH' or 'SUP')
and screen_stage (1 for primary, 2 for secondary).
"""
worms = WormStrain.get_worms_for_screen_type(screen_type)
all_positives = set()
for worm in worms:
positives = worm.get_positives(screen_type, screen_stage, criteria,
**kwargs)
all_positives = all_positives.union(positives)
return all_positives
def get_positives_any_worm(screen_type, screen_stage, criteria, **kwargs):
"""
Get the set of library stocks that are positive for ANY worm.
A screen is defined by both screen_type ('ENH' or 'SUP')
and screen_stage (1 for primary, 2 for secondary).
"""
worms = WormStrain.get_worms_for_screen_type(screen_type)
all_positives = set()
for worm in worms:
positives = worm.get_positives(screen_type, screen_stage, criteria,
**kwargs)
all_positives = all_positives.union(positives)
return all_positives
def _limit_to_screen_type(experiments, screen_type):
"""
Post-process experiments QuerySet such that each experiment was done at its
worm's SUP or ENH temperature. Since N2 does not have a SUP or ENH
temperature, N2 will not be in this result.
Question: Why not just get the SUP/ENH temperature for these experiments'
worm, and then using `.filter()` with that temperature?
Answer: That is what I do on queries limited to a single worm strain, e.g.
for most of the public-facing pages. But these experiment filtering forms
are meant to be flexible (basically a gateway into the database for GI
team use only), flexible enough to potentially include multiple strains
with different SUP/ENH temperatures (e.g. maybe Noah wants to see all
experiments from one date).
Question: Why not just join between ExperimentPlate.temperature and
WormStrain.permissive_temperature / .restrictive_temperature?
This would involve joining WormStrain on a second field. While easy with
raw SQL, this is not easy with Django, requiring either 1) soon-to-
be-deprecated `empty()`, 2) overriding low level query processing in ways
that are subject to syntax changes, or 3) using `raw()` to write raw SQL.
While I was tempted to do 3), since these filtering forms are meant to be
generic and applicable (able to take dozens of possible keys to filter on),
this one case doesn't warrant losing the readability and protections
against SQL injection attacks that Django QuerySets provide.
"""
# Create a dictionary
to_temperature = WormStrain.get_worm_to_temperature_dictionary(screen_type)
filtered = []
for experiment in experiments.prefetch_related("worm_strain", "plate"):
temperature = experiment.plate.temperature
if temperature == to_temperature[experiment.worm_strain]:
filtered.append(experiment)
return filtered
def clean_mutant_query_and_screen_type(form, cleaned_data):
"""
Helper to derive worm strain and temperature from cleaned_data.
If cleaned_data['mutant_query'] and cleaned_data['screen_type']
are defined, cleaned_data['worm'] and cleaned_data['temperature']
will be populated.
Returns the modified cleaned_data.
"""
mutant_query = cleaned_data.get('mutant_query')
screen_type = cleaned_data.get('screen_type')
if mutant_query and screen_type:
worm_and_temp = WormStrain.get_worm_and_temperature_from_search_term(
mutant_query, screen_type)
if worm_and_temp:
cleaned_data['worm'] = worm_and_temp[0]
cleaned_data['temperature'] = worm_and_temp[1]
else:
form.add_error('mutant_query', 'No mutant match')
return cleaned_data
def get_n2_control_filters(self):
"""
Get the N2 + RNAi controls for this experiment.
To get the actual control experiments from the returned filters,
simply do Experiment.objects.filter(**filters). Returning
the filters is more flexible for customization, or for inserting
into a URL without performing the query.
N2 controls for this experiment are restricted to those from
the same date, *closest* temperature, same RNAi clone.
"""
filters = {
'is_junk': False,
'plate__date': self.date(),
'plate__temperature': self.temperature(),
'library_stock': self.library_stock,
'worm_strain': WormStrain.get_n2().pk,
}
filters['plate__temperature'] = Experiment.get_closest_temperature(
self.temperature(), filters)
return filters
def double_knockdown(request, mutant, clones, temperature):
"""
Render the page showing knockdown by both mutation and RNAi.
context['data'] is returned in format:
{clone: {
library_stock: {
date: {
'mutant_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'n2_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'mutant_l4440': {
'experiments': [experiments], 'link_to_all': url
},
'n2_l4440': {
'experiments': [experiments], 'link_to_all': url
},
}
}
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
l4440 = Clone.get_l4440()
mutant = get_object_or_404(WormStrain, pk=mutant)
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
data_per_clone = OrderedDict()
library_stocks = (LibraryStock.objects.filter(
intended_clone=clone).order_by('-plate__screen_stage', 'id'))
for library_stock in library_stocks:
data_per_well = OrderedDict()
dates = Experiment.get_distinct_dates({
'is_junk':
False,
'worm_strain':
mutant,
'library_stock':
library_stock,
'plate__temperature':
temperature,
})
for date in dates:
# Add double knockdowns
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock': library_stock,
'plate__temperature': temperature,
}
mutant_rnai = _create_inner_dictionary(filters,
join_manual=True)
# Add mutant + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock__intended_clone': l4440,
'plate__temperature': temperature,
}
mutant_l4440 = _create_inner_dictionary(filters)
# Add N2 + RNAi controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock': library_stock,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_rnai = _create_inner_dictionary(filters)
# Add N2 + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock__intended_clone': l4440,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_l4440 = _create_inner_dictionary(filters)
data_per_well[date] = {
'mutant_rnai': mutant_rnai,
'mutant_l4440': mutant_l4440,
'n2_rnai': n2_rnai,
'n2_l4440': n2_l4440,
}
if data_per_well:
data_per_clone[library_stock] = data_per_well
data[clone] = data_per_clone
context = {
'mutant': mutant,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'double_knockdown.html', context)
def double_knockdown(request, mutant, clones, temperature):
"""
Render the page showing knockdown by both mutation and RNAi.
context['data'] is returned in format:
{clone: {
library_stock: {
date: {
'mutant_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'n2_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'mutant_l4440': {
'experiments': [experiments], 'link_to_all': url
},
'n2_l4440': {
'experiments': [experiments], 'link_to_all': url
},
}
}
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
l4440 = Clone.get_l4440()
mutant = get_object_or_404(WormStrain, pk=mutant)
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
data_per_clone = OrderedDict()
library_stocks = (LibraryStock.objects.filter(intended_clone=clone)
.order_by('-plate__screen_stage', 'id'))
for library_stock in library_stocks:
data_per_well = OrderedDict()
dates = Experiment.get_distinct_dates({
'is_junk': False,
'worm_strain': mutant,
'library_stock': library_stock,
'plate__temperature': temperature,
})
for date in dates:
# Add double knockdowns
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock': library_stock,
'plate__temperature': temperature,
}
mutant_rnai = _create_inner_dictionary(
filters, join_manual=True)
# Add mutant + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock__intended_clone': l4440,
'plate__temperature': temperature,
}
mutant_l4440 = _create_inner_dictionary(filters)
# Add N2 + RNAi controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock': library_stock,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_rnai = _create_inner_dictionary(filters)
# Add N2 + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock__intended_clone': l4440,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_l4440 = _create_inner_dictionary(filters)
data_per_well[date] = {
'mutant_rnai': mutant_rnai,
'mutant_l4440': mutant_l4440,
'n2_rnai': n2_rnai,
'n2_l4440': n2_l4440,
}
if data_per_well:
data_per_clone[library_stock] = data_per_well
data[clone] = data_per_clone
context = {
'mutant': mutant,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'double_knockdown.html', context)
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)
def test_get_n2(self):
n2 = WormStrain.get_n2()
self.assertEquals(n2.id, 'N2')
self.assertIsNone(n2.permissive_temperature)
self.assertIsNone(n2.restrictive_temperature)