def test_parsing(self):
"""parsing should return model descriptions"""
obo = MinimalObo(obo_file)
models = prep_IMPC(impc_file, (0.8, 0.05), 0.01, obo=obo)
# should get eight models
# two marker, two allele; one zygosity
# one set of 4 with positive phenoytpes,
# one set of 4 with negative phenotypes
# that is 8. Then x3 for universal/male/female
self.assertEqual(len(models), 24)
alleles = set()
markers = set()
for _, value in models.items():
alleles.add(value.description["allele_id"])
markers.add(value.description["marker_id"])
self.assertEqual(len(alleles), 2)
self.assertEqual(len(markers), 2)
# count the male and female models
males, females, unspecified = 0, 0, 0
for _, value in models.items():
sex = value.description["sex"]
if sex == "M":
males += 1
elif sex == "F":
females += 1
elif sex:
unspecified += 1
self.assertEqual(males, females, "should be paired and equal")
self.assertEqual(males, unspecified, "should be paired and equal")
self.assertGreater(males, 0)
def test_scaled_cooc(self):
"""write out cooc matrices"""
obo = MinimalObo(obo_file)
models = prep_IMPC(impc_file, (0.8, 0.05), 0.01, obo=obo)
models_allele = get_UA_models(models, "allele")
observed = get_models_by_phenotype(models_allele, 1)
# write out various types of cooc matrices
cooc_full, phenindex = make_scaled_cooc(observed, obo, 0, "full")
write_phenotype_cooc(cooc_full, phenindex, out_prefix + "-full")
cooc_freq, phenindex = make_scaled_cooc(observed, obo, 0, "freq")
write_phenotype_cooc(cooc_freq, phenindex, out_prefix + "-freq")
cooc_simJ, phenindex = make_scaled_cooc(observed, obo, 0, "simJ")
write_phenotype_cooc(cooc_simJ, phenindex, out_prefix + "-simJ")
# check the numerics of the matrices
for p1, i1 in phenindex.items():
for p2, i2 in phenindex.items():
observed = cooc_full[i1, i2]
expected = cooc_freq[i1, i2] * (1 - cooc_simJ[i1, i2])
self.assertEqual(observed, expected)
# check all the files exist
self.assertTrue(exists(cooc_full_file))
self.assertTrue(exists(cooc_freq_file))
self.assertTrue(exists(cooc_simJ_file))
# very gently (not rigorously check content of files)
with open_file(cooc_full_file, "rt") as f:
full = f.read().strip().split("\n")
self.assertGreater(len(full), 2)
def test_writing(self):
"""write the parsed MGI data onto files"""
obo = MinimalObo(obo_file)
models = prep_IMPC(impc_file, (0.8, 0.05), 0.01, obo=obo)
write_models(models, out_prefix)
# read contents back
self.assertTrue(exists(desc_file))
self.assertTrue(exists(pheno_file))
with open_file(desc_file, "rt") as f:
desc = f.read().strip().split("\n")
with open_file(pheno_file, "rt") as f:
pheno = f.read().strip().split("\n")
# description file should have 25 lines, 24 data lines plus header
self.assertEqual(len(desc), 25)
# phenotype file should have at least 7 lines (more)
self.assertGreater(len(pheno), 7)
def test_imputing(self):
"""create new models based on UA."""
obo = MinimalObo(obo_file)
models = prep_IMPC(impc_file, (0.8, 0.05), 0.01, obo=obo)
models_allele = get_UA_models(models, "allele")
imputed = impute_IMPC(models_allele, obo, 0)
write_models(imputed, out_prefix + "-imputed")
# check output files exist and contain proper content
self.assertTrue(exists(imputed_desc_file))
self.assertTrue(exists(imputed_pheno_file))
with open_file(imputed_desc_file, "rt") as f:
desc = f.read().strip().split("\n")
with open_file(imputed_pheno_file, "rt") as f:
pheno = f.read().strip().split("\n")
# description file should have 3 lines, 2 desc lines plus header
self.assertEqual(len(desc), 3)
# phenotype file should have a few lines
self.assertGreater(len(pheno), 3)
def test_parsing_empty(self):
"""parsing empty input return empty dict"""
result = prep_IMPC(None, None, None)
self.assertEqual(result, dict())
priors, num_models = get_priors_from_models(models,
categories,
obo,
dark=config.dark_count)
print("Number of models used to inform prior: " + str(num_models))
write_priors(priors, config.output)
if config.action == "IMPC":
# action to parse mouse model annotations from IMPC
check_file(config.input, required="input")
check_file(config.obo)
obo = MinimalObo(config.obo)
models = prep_IMPC(config.input,
tprfpr,
threshold,
simplify=config.simplify,
obo=obo)
# filter functions
def f_U_allele(x):
return x.category == "allele" and x.description["sex"] == "U"
def f_S_allele(x):
return x.category == "allele" and x.description["sex"] != "U"
def f_U_marker(x):
return x.category == "marker" and x.description["sex"] == "U"
def f_S_marker(x):
return x.category == "marker" and x.description["sex"] != "U"