def main():
client = utils.get_mongo_client()
db = utils.get_database(client, 'omni')
path = 'data/TSO500_UniqueVariants_runs1-6.csv'
# path = 'data/TSO500_UniqueVariants_4.csv'
var_list = TSO500.read_tso_unique_variants(path)
outF = open("data/decisions.tsv", "w")
h = "gene\tcdot\tpdot\tgene_category\tmutation_type\treport_status\treasons\tlack_of_reasons\t" \
"is_protein_altering\tin_clinvar\tis_clinvar_benign\tis_clinvar_pathogenic\tclinvar_explain\t" \
"is_gain_of_function\tis_loss_of_function\thotspots\tpredicted_deleterious\tis_truncating_variants\tis_near_GOF_LOF_mutation\t" \
"omni_gene\tomni_cdot\tomni_pdot"
# print(h)
outF.write(h)
outF.write("\n")
for index, variant in enumerate(var_list):
key = get_key_from_variant(variant)
annotated = get_annotated_snv(key, db)
if not 'reasons' in annotated:
annotated['reasons'] = []
if not 'lack_of_reasons' in annotated:
annotated['lack_of_reasons'] = []
is_tso_snv_reportable(annotated)
s = f"{annotated['gene']}\t{annotated['cdot']}\t{annotated['pdot']}\t{annotated['gene_category']}\t{annotated['mutation_type']}\t" \
f"{annotated['report_status']}\t{annotated['reasons']}\t{annotated['lack_of_reasons']}\t" \
f"{annotated['is_protein_altering']}\t{annotated['in_clinvar']}\t{annotated['is_clinvar_benign']}\t{annotated['is_clinvar_pathogenic']}\t{annotated['clinvar_explain']}\t" \
f"{annotated['is_gain_of_function']}\t{annotated['is_loss_of_function']}\t{annotated['hotspots']}\t{annotated['predicted_deleterious']}\t" \
f"{annotated['is_truncating_variants']}\t{annotated['is_near_GOF_LOF_mutation']}\t" \
f"{annotated['HGNC_Symbol']}\t{annotated['omni_c_dot']}\t{annotated['omni_p_dot']}"
# print(s)
outF.write(s)
outF.write("\n")
outF.close()
def main():
empty_output_dir()
client = utils.get_mongo_client()
db = utils.get_database(client, 'omni')
fake_id_dict = read_variants.read_fake_ids()
disease_icd_dict = read_variants.read_disease_icd_dict()
omni_to_jax_disease_dict = read_variants.read_omni_to_jax_disease_dict()
disease_path_to_reportable_disease_dict = read_variants.read_omni_reportable_disease_name_dict(
)
variant_groups_dict = read_variants.read_variant_groups_dict()
io_drug_dict = additional_io.get_io_drug_dict()
patients = read_variants.read_immune_results_file(
get_immune_results_file_path())
read_variants.read_all_variants(patients, get_variant_file_path())
read_variants.read_summary_interprations(patients, get_summary_file_path())
strands = annotate.read_strands('data/strands.xlsx')
num = 1
with open('output/manifest.txt', "w") as file:
for order_id in patients.keys():
patient = patients[order_id]
read_variants.add_patient_data(
patient, fake_id_dict, disease_icd_dict,
omni_to_jax_disease_dict,
disease_path_to_reportable_disease_dict)
handle_one_patient(patient, db, strands, variant_groups_dict,
io_drug_dict)
# create_recommendations(patient,db)
create_one_report(patient)
out_string = generate_manifest_string(num, order_id, patient)
print(out_string)
# file.write(out_string)
num += 1
def retrieve_all_player_ranks():
mongo_client = get_mongo_client()
database = mongo_client["tennis"]
collection = database["player_ranks"]
player_ranks = pd.DataFrame(list(collection.find({}, {'_id': False})))
return player_ranks
def record_all_player_ranks(player_ranks):
mongo_client = get_mongo_client()
database = mongo_client["tennis"]
collection = database["player_ranks"]
# Remove previous ranks
collection.remove()
# Insert new ranks
records = player_ranks.to_dict(orient='records')
result = collection.insert_many(records)
return result.acknowledged
def main():
client = utils.get_mongo_client()
db = utils.get_database(client,'omni')
path = 'data/TSO500_UniqueVariants_runs1-6.csv'
# path = 'data/TSO500_UniqueVariants_4.csv'
var_list = TSO500.read_tso_unique_variants(path)
variants_to_analyze = []
for index, variant in enumerate(var_list):
key = get_key_from_variant(variant)
annotated = get_annotated_snv(key,db)
if annotated == None:
variants_to_analyze.append(variant)
if len(variants_to_analyze) >= 100:
report_on_variants(db, variants_to_analyze)
variants_to_analyze = []
if len(variants_to_analyze)>0:
report_on_variants(db, variants_to_analyze)
def get_tournament_collection():
mongo_client = get_mongo_client()
database = mongo_client["tennis"]
return database["tournaments"]
def get_matches_collection():
mongo_client = get_mongo_client()
database = mongo_client["tennis"]
return database["matches"]
def get_player_collection():
mongo_client = get_mongo_client()
database = mongo_client["tennis"]
return database["players"]
def get_country_collection():
mongo_client = get_mongo_client()
database = mongo_client["tennis"]
return database["countries"]
def get_log_collection():
myclient = get_mongo_client()
mydb = myclient["tennis"]
return mydb["logs"]