def make_variant_probe(al, variant, kmer, DB=None, no_backgrounds=False):
if no_backgrounds:
context = []
else:
if DB is not None:
try:
context = get_context(variant.start, kmer)
except:
DB = None
context = []
logger.warning(
"Could not connect to database. Continuing without using backgrounds"
)
else:
context = []
if context:
logger.debug("Found %i variants in context of %s" %
(len(context), variant))
variant_probe = None
contexts_seen_together = seen_together(context)
alts = []
for context in contexts_seen_together:
if context:
logger.debug("Processing variant:%s with context:%s" %
(variant, ",".join([str(c) for c in context])))
else:
logger.debug("Processing variant:%s " % (variant))
try:
panel = al.create(variant, context)
except ValueError as e:
pass
logger.warning("Failed to process variant:%s context:%s. %s" %
(variant, ",".join([str(c)
for c in context]), str(e)))
else:
if variant_probe is not None:
variant_probe.alts.extend(panel.alts)
variant_probe.refs.extend(panel.refs)
else:
variant_probe = panel
if variant_probe:
variant_probe.alts = unique(variant_probe.alts)
variant_probe.refs = unique(variant_probe.refs)
return variant_probe
def diff(self, other):
diff = {}
# Compares the antibiogram of two predictor results
drugs = unique(self.drugs + other.drugs)
for drug in drugs:
predict1, predict2 = self.susceptibility.get(drug, {"predict": "NA"}).get(
"predict"), other.susceptibility.get(drug, {"predict": "NA"}).get("predict")
if predict1 != predict2:
diff[drug] = {}
diff[drug]["predict"] = (predict1, predict2)
return diff
def create_comparision_table(sample_ids, truth, ana1, ana2, ignore_drugs=[]):
df = []
for sample_id in sample_ids:
indv_truth = truth.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
indv_ana1 = ana1.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
indv_ana2 = ana2.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
drugs = unique(indv_truth.drugs + indv_ana1.drugs + indv_ana2.drugs)
if drugs:
for drug in drugs:
if drug not in ignore_drugs:
if args.ana2:
row = [
sample_id, drug, indv_truth.susceptibility.get(
drug, {
"predict": "NA"}).get("predict"), indv_ana1.susceptibility.get(
drug, {
"predict": "NA"}).get("predict"), indv_ana2.susceptibility.get(
drug, {
"predict": "NA"}).get("predict")]
else:
row = [
sample_id, drug, indv_truth.susceptibility.get(
drug, {
"predict": "NA"}).get("predict"), indv_ana1.susceptibility.get(
drug, {
"predict": "NA"}).get("predict")]
df.append(row)
return df
def create_comparision_table(sample_ids, truth, ana1, ana2, ignore_drugs=[]):
df = []
for sample_id in sample_ids:
indv_truth = truth.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
indv_ana1 = ana1.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
indv_ana2 = ana2.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
drugs = unique(indv_truth.drugs + indv_ana1.drugs + indv_ana2.drugs)
if drugs:
for drug in drugs:
if drug not in ignore_drugs:
if args.ana2:
row = [
sample_id, drug, indv_truth.susceptibility.get(
drug, {
"predict": "NA"}).get("predict"), indv_ana1.susceptibility.get(
drug, {
"predict": "NA"}).get("predict"), indv_ana2.susceptibility.get(
drug, {
"predict": "NA"}).get("predict")]
else:
row = [
sample_id, drug, indv_truth.susceptibility.get(
drug, {
"predict": "NA"}).get("predict"), indv_ana1.susceptibility.get(
drug, {
"predict": "NA"}).get("predict")]
df.append(row)
return df
def _get_drug_list_from_variant_to_resistance_drug(self):
return unique(
flatten(self.variant_or_gene_name_to_resistance_drug.values()))
def compare_analysis_to_truth(sample_ids, truth, ana, ana_name=""):
comparison = {}
for sample_id in sample_ids:
indv_truth = truth.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
indv_ana = ana.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
drugs = unique(indv_truth.drugs + indv_ana.drugs)
try:
[drugs.remove(d) for d in args.ignore_drugs]
except:
pass
if drugs:
for drug in drugs:
if drug == "Fusidicacid":
drug = "FusidicAcid"
truth_drug_predict = indv_truth.susceptibility.get(
drug, {"predict": "NA"}).get("predict").upper().strip()[0]
ana_drug_predict = indv_ana.susceptibility.get(
drug, {"predict": "NA"}).get("predict").upper().strip()[0]
ana_drug_predict = ana_drug_predict.replace(
"INCONCLUSIVE", "I")
truth_drug_predict = truth_drug_predict.replace(
"INCONCLUSIVE", "I")
truth_drug_predict = truth_drug_predict.replace("B", "I")
truth_drug_predict = truth_drug_predict.replace("N", "I")
ana_drug_predict = ana_drug_predict.replace("N", "I")
truth_drug_predict = truth_drug_predict.replace("IA", "I")
if not truth_drug_predict in ["R", "NA", "S", "I"]:
sys.stderr.write(
"failed truth check %s %s - %s - %s \n" %
(ana_name, sample_id, drug, truth_drug_predict))
elif ana_drug_predict not in ["R", "NA", "S", "I"]:
sys.stderr.write(
"failed predict check %s %s - %s - %s \n" %
(ana_name, sample_id, drug, ana_drug_predict))
else:
if truth_drug_predict == "NA":
compare = "UNKNOWN"
elif ana_drug_predict == "I" or ana_drug_predict == "NA":
if truth_drug_predict == "R":
compare = "IR"
elif truth_drug_predict == "S":
compare = "IS"
else:
compare = "UNKNOWN"
elif truth_drug_predict == ana_drug_predict:
if truth_drug_predict == "R":
compare = "TP"
elif truth_drug_predict == "S":
compare = "TN"
else:
compare = "UNKNOWN"
else:
if truth_drug_predict == "R":
compare = "FN"
elif truth_drug_predict == "S":
compare = "FP"
else:
compare = "UNKNOWN"
comparison = update_comparision(comparison, drug, compare)
return comparison
def get_union_sample_ids(ana1, ana2):
return unique(ana1.keys() + ana2.keys())
def compare_analysis_to_truth(sample_ids, truth, ana, ana_name=""):
comparison = {}
for sample_id in sample_ids:
indv_truth = truth.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
indv_ana = ana.get(
sample_id,
MykrobePredictorSusceptibilityResult.create(
{}))
drugs = unique(indv_truth.drugs + indv_ana.drugs)
try:
[drugs.remove(d) for d in args.ignore_drugs]
except:
pass
if drugs:
for drug in drugs:
if drug == "Fusidicacid":
drug = "FusidicAcid"
truth_drug_predict = indv_truth.susceptibility.get(
drug, {"predict": "NA"}).get("predict").upper().strip()[0]
ana_drug_predict = indv_ana.susceptibility.get(
drug, {"predict": "NA"}).get("predict").upper().strip()[0]
ana_drug_predict = ana_drug_predict.replace(
"INCONCLUSIVE", "I")
truth_drug_predict = truth_drug_predict.replace(
"INCONCLUSIVE", "I")
truth_drug_predict = truth_drug_predict.replace("B", "I")
truth_drug_predict = truth_drug_predict.replace("N", "I")
ana_drug_predict = ana_drug_predict.replace("N", "I")
truth_drug_predict = truth_drug_predict.replace("IA", "I")
if not truth_drug_predict in ["R", "NA", "S", "I"]:
sys.stderr.write(
"failed truth check %s %s - %s - %s \n" %
(ana_name, sample_id, drug, truth_drug_predict))
elif ana_drug_predict not in ["R", "NA", "S", "I"]:
sys.stderr.write(
"failed predict check %s %s - %s - %s \n" %
(ana_name, sample_id, drug, ana_drug_predict))
else:
if truth_drug_predict == "NA":
compare = "UNKNOWN"
elif ana_drug_predict == "I" or ana_drug_predict == "NA":
if truth_drug_predict == "R":
compare = "IR"
elif truth_drug_predict == "S":
compare = "IS"
else:
compare = "UNKNOWN"
elif truth_drug_predict == ana_drug_predict:
if truth_drug_predict == "R":
compare = "TP"
elif truth_drug_predict == "S":
compare = "TN"
else:
compare = "UNKNOWN"
else:
if truth_drug_predict == "R":
compare = "FN"
elif truth_drug_predict == "S":
compare = "FP"
else:
compare = "UNKNOWN"
comparison = update_comparision(comparison, drug, compare)
return comparison
def get_union_sample_ids(ana1, ana2):
return unique(ana1.keys() + ana2.keys())
def _get_drug_list_from_variant_to_resistance_drug(self):
return unique(flatten(self.variant_or_gene_name_to_resistance_drug.values()))
