import pandas as pd
from catalog_preparation.catalog_creation_helper import remove_literally, all_cases_of_cases
food_file_path = '../data/food/food.tsv'
output_csv_path = '../data/food/food_usda_tidy.csv'
if __name__ == '__main__':
food_data = pd.read_table(food_file_path, sep=';', encoding='cp1252', header=1, names=['group', 'name'])
food_data = remove_literally(food_data, ['pie'])
food_data_cases = all_cases_of_cases(food_data)
food_data = pd.merge(food_data, food_data_cases, on=list(food_data), how='outer')
food_data = food_data.drop_duplicates()
food_data.to_csv(output_csv_path, index=False)
synonyms = []
try:
groups = [group.value for group in stanza.tags['is_a']]
except:
groups = ['NA']
names = [name] + synonyms
# apostrophe1_names = [name.replace('\'', '’') for name in names if '\'' in name]
# apostrophe2_names = [name.replace('’', '\'') for name in names if '’' in name]
names = [re.sub('[’\']', '', name) for name in names]
for disease_name in names:
for group in groups:
entry = {'id': disease_id,
'name': disease_name,
'group': group,
'obsolete': is_obsolete}
disease_data = disease_data.append(entry, ignore_index=True)
return disease_data
obo_path = "../data/diseases/doid.obo"
output_path = '../data/diseases/diseases_catalog.csv'
if __name__ == '__main__':
disease_data = parse_obo(obo_path)
disease_data = remove_literally(disease_data, ['disease'])
disease_data_cases = all_cases_of_cases(disease_data)
disease_data = pd.merge(disease_data, disease_data_cases, on=list(disease_data), how='outer')
disease_data = disease_data.drop_duplicates()
disease_data.to_csv(output_path, index=False, sep='\t')
