def test_external_reference():
experiments = fcmcmp.load_experiments(dummy_data / "external_reference.yml")
assert experiments[0]["label"] == "sgGFP"
assert experiments[0]["channel"] == "FITC-A"
check_wells(experiments, before=["A1"], after=["B1"])
def test_specify_both_plates():
experiments = fcmcmp.load_experiments(dummy_data / "specify_both_plates.yml")
assert experiments[0]["label"] == "sgNull"
assert experiments[0]["channel"] == "FSC-A"
check_wells(experiments, before=["p1/A1", "p2/A1"], after=["p1/B1", "p2/B1"])
def test_specify_plate_1():
experiments = fcmcmp.load_experiments(dummy_data / 'specify_plate_1.yml')
assert experiments[0]['label'] == 'sgRFP'
assert experiments[0]['channel'] == 'PE-Texas Red-A'
check_wells(experiments, before=['A1'], after=['B1'])
def test_specify_plate_1():
experiments = fcmcmp.load_experiments(dummy_data / "specify_plate_1.yml")
assert experiments[0]["label"] == "sgRFP"
assert experiments[0]["channel"] == "PE-Texas Red-A"
check_wells(experiments, before=["A1"], after=["B1"])
def test_infer_plate_1():
experiments = fcmcmp.load_experiments(dummy_data / 'plate_1.yml')
assert experiments[0]['label'] == 'sgGFP'
assert experiments[0]['channel'] == 'FITC-A'
check_wells(experiments, before=['A1'], after=['B1'])
def test_infer_plate_1():
experiments = fcmcmp.load_experiments(dummy_data / "plate_1.yml")
assert experiments[0]["label"] == "sgGFP"
assert experiments[0]["channel"] == "FITC-A"
check_wells(experiments, before=["A1"], after=["B1"])
def calc_fold_changes(rebuild_cache=False):
json_path = Path('fold_changes.json')
fcm_path = Path('../../../data/facs/20180312_library_hits_with_tpp.yml')
# Cache the fold changes because they take a while to calculate.
try:
if rebuild_cache:
raise FileNotFoundError
with json_path.open() as file:
return json.load(file)
except (FileNotFoundError, json.JSONDecodeError):
fold_changes = {}
experiments = fcmcmp.load_experiments(fcm_path)
shared_steps = analysis_helpers.SharedProcessingSteps()
shared_steps.process(experiments)
analysis_helpers.analyze_wells(experiments)
for pair in analysis_helpers.yield_related_wells(experiments):
fold_change, _ = pair.calc_fold_change_with_sign()
if fold_change < 1:
fold_changes[pair.label] = 1/fold_change, False
else:
fold_changes[pair.label] = fold_change, True
with json_path.open('w') as file:
json.dump(fold_changes, file)
return fold_changes
def test_external_reference():
experiments = fcmcmp.load_experiments(dummy_data /
'external_reference.yml')
assert experiments[0]['label'] == 'sgGFP'
assert experiments[0]['channel'] == 'FITC-A'
check_wells(experiments, before=['A1'], after=['B1'])
def test_multiple_experiments():
experiments = fcmcmp.load_experiments(dummy_data / "multiple_experiments.yml")
assert experiments[0]["label"] == "sgGFP"
assert experiments[0]["channel"] == "FITC-A"
assert experiments[1]["label"] == "sgRFP"
assert experiments[1]["channel"] == "PE-Texas Red-A"
check_wells(experiments, before=["A1"], after=["B1"])
def test_multiple_experiments():
experiments = fcmcmp.load_experiments(dummy_data /
'multiple_experiments.yml')
assert experiments[0]['label'] == 'sgGFP'
assert experiments[0]['channel'] == 'FITC-A'
assert experiments[1]['label'] == 'sgRFP'
assert experiments[1]['channel'] == 'PE-Texas Red-A'
check_wells(experiments, before=['A1'], after=['B1'])
def test_specify_both_plates():
experiments = fcmcmp.load_experiments(dummy_data /
'specify_both_plates.yml')
assert experiments[0]['label'] == 'sgNull'
assert experiments[0]['channel'] == 'FSC-A'
check_wells(experiments,
before=['p1/A1', 'p2/A1'],
after=['p1/B1', 'p2/B1'])
def test_unspecified_plate():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'unspecified_plate.yml')
assert "No default plate defined" in str(exc_info.value)
def test_ambiguous_well():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'ambiguous_well.yml')
assert "Multiple *.fcs files found for well" in str(exc_info.value)
def test_nonexistent_well():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'nonexistent_well.yml')
assert "No *.fcs files found for well" in str(exc_info.value)
def test_missing_wells():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'missing_wells.yml')
assert "doesn't have any wells" in str(exc_info.value)
def test_missing_label():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'missing_label.yml')
assert "missing a label" in str(exc_info.value)
def test_ambiguous_header():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "ambiguous_header.yml")
assert "Too many fields in 'plates' header." in str(exc_info.value)
def test_missing_label():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "missing_label.yml")
assert "missing a label" in str(exc_info.value)
def test_missing_wells():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "missing_wells.yml")
assert "doesn't have any wells" in str(exc_info.value)
def test_empty_experiment():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "empty_experiment.yml")
assert "empty experiment was found" in str(exc_info.value)
def test_nonexistent_well():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "nonexistent_well.yml")
assert "No *.fcs files found for well" in str(exc_info.value)
def test_ambiguous_well():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "ambiguous_well.yml")
assert "Multiple *.fcs files found for well" in str(exc_info.value)
def test_unspecified_plate():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "unspecified_plate.yml")
assert "No default plate defined" in str(exc_info.value)
def test_undefined_plate():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'undefined_plate.yml')
assert "Plate 'foo' not defined." in str(exc_info.value)
def test_empty_file():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'empty_file.yml')
assert "is empty" in str(exc_info.value)
def test_ambiguous_header():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'ambiguous_header.yml')
assert "Too many fields in 'plates' header." in str(exc_info.value)
def test_empty_experiment():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / 'empty_experiment.yml')
assert "empty experiment was found" in str(exc_info.value)
def test_empty_file():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "empty_file.yml")
assert "is empty" in str(exc_info.value)
def test_undefined_plate():
with pytest.raises(fcmcmp.UsageError) as exc_info:
fcmcmp.load_experiments(dummy_data / "undefined_plate.yml")
assert "Plate 'foo' not defined." in str(exc_info.value)
if self.verbose:
label = f"{experiment['label']} {condition} [{well.label}]"
net_time = times.iloc[-1] - times.iloc[0]
net_rate = len(times) / net_time
print(f"{label:40s}\t{net_rate:.2f} evt/sec")
plt.xlim(min_time, max_time)
plt.ylim(0, plt.ylim()[1])
plt.xlabel('Collection time (sec)')
plt.ylabel('Events/sec')
if self.keyword:
plt.title(self.keyword)
if self.show_legend:
plt.legend(loc='best')
if __name__ == '__main__':
args = docopt.docopt(__doc__)
experiments = fcmcmp.load_experiments(args['<yml_path>'])
analysis = EventsPerSec(experiments)
analysis.keyword = args['<keyword>']
analysis.show_legend = args['--show-legend']
analysis.time_window = float(args['--time-window'])
analysis.verbose = args['--verbose']
with analysis_helpers.plot_or_savefig(args['--output'],
args['<yml_path>']):
analysis.plot()
# Yield a cell for each combination of construct and spacer.
yield (x, y), construct, spacer
# See if this construct has any unexpected mutations, and if it
# does, also yield a cell that excludes them.
expected_only = construct + ',1'
y_offset = self.cell_height * (len(self.spacers) + 1 / 2)
if design_exists(expected_only):
yield (x, y - y_offset), expected_only, spacer
class DataMissing(Exception):
pass
initial_picks = fcmcmp.load_experiments(
'../../results/facs/20160727_screen_mhf.yml')
recloned_hits = fcmcmp.load_experiments(
'../../results/facs/20160923_test_mhf_hits.yml')
shared_steps = analysis_helpers.SharedProcessingSteps()
shared_steps.process(initial_picks + recloned_hits)
def get_fold_change(construct, spacer):
expt = find_experiment(construct, spacer)
apo_well = analysis_helpers.AnalyzedWell(expt, expt['wells']['apo'][0])
holo_well = analysis_helpers.AnalyzedWell(expt, expt['wells']['holo'][0])
xlim = 0, 5
apo_well.estimate_distribution(xlim)
holo_well.estimate_distribution(xlim)