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import os
import pandas as pd
from string import Template
from dateutil.parser import parse
import sys
sys.path.append('../')
from utils import check_and_get_ontology_dictionaries
# Metadata in tabular format
path_metadata_xlsx = 'Pathogen.cl.1.0.xlsx'
path_template_yaml = 'template.yaml'
# Removed from the template (for now)
# license:
# license_type: "http://creativecommons.org/licenses/by/4.0/"
# title: "SARS-CoV-2 New Zealand"
# attribution_name: "ESR"
# attribution_url: "https://www.esr.cri.nz/"
# Read the dictionaries for the ontology
dir_dict_ontology_standardization = '../dict_ontology_standardization/'
field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization)
dir_output = 'yaml'
suffix = '.consensus'
if not os.path.exists(dir_output):
os.makedirs(dir_output)
metadata_df = pd.read_excel(path_metadata_xlsx, skiprows=12)
# Maybe not the best pandas-way to do this
for index, row in metadata_df.iterrows():
# print(row['*sample_name'])
geo_loc_name = row['*geo_loc_name'].replace(': ', ':')
if geo_loc_name not in field_to_term_to_uri_dict['ncbi_countries']:
if geo_loc_name in [
'New Zealand:Counties Manukau', 'New Zealand:Capital and Coast', 'New Zealand:Southern',
'New Zealand:Waikato',
'New Zealand:Lakes', 'New Zealand:Nelson Marlborough', 'New Zealand:South Canterbury',
'New Zealand:MidCentral',
'New Zealand:Tairawhiti', 'New Zealand:Hawkes Bay', 'New Zealand:NA', 'New Zealand:Taranaki'
]:
geo_loc_name = 'New Zealand'
else:
print(geo_loc_name)
break
country = field_to_term_to_uri_dict['ncbi_countries'][geo_loc_name]
d = {
'host_species': field_to_term_to_uri_dict['ncbi_host_species'][row['*host']],
'sample_id': row['*sample_name'],
'collection_date': parse(row['*collection_date']).strftime('%Y-%m-%d'),
'collection_location': country,
'specimen_source': field_to_term_to_uri_dict['ncbi_speciesman_source'][row['*isolation_source']],
'virus_species': 'http://purl.obolibrary.org/obo/NCBITaxon_2697049',
'submitter_sample_id': row['bioproject_accession'],
}
with open(path_template_yaml) as f:
src = Template(f.read())
with open(os.path.join(dir_output, '{}{}.yaml'.format(row['*sample_name'], suffix)), 'w') as fw:
fw.write(src.substitute(d))
print('{} YAML files created.'.format(len([x for x in os.listdir(dir_output) if x.endswith('.yaml')])))
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