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update geography_cleaning to take an argument for central_sample_id (… #5

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update geography_cleaning to take an argument for central_sample_id (… #5

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13 changes: 7 additions & 6 deletions geography_cleaning.py
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Original file line number Diff line number Diff line change
Expand Up @@ -379,7 +379,7 @@ def deal_with_nonuk_cog(country, adm1, adm2, epiweek, geog_dict, adm2_to_week_co
return geog_dict, adm2_to_week_counts


def process_input(metadata_file, country_col, outer_postcode_col, adm1_col, adm2_col, epiweek_col, map_utils_dir,outdir):
def process_input(metadata_file, country_col, outer_postcode_col, adm1_col, adm2_col, epiweek_col, sample_id_col, map_utils_dir,outdir):

outer_to_latlongs_region = find_outerpostcode_to_coord_mapping(map_utils_dir)
metadata_multi_loc, straight_map = prep_adm2_data(os.path.join(map_utils_dir, "adm2_cleaning.tsv"))
Expand Down Expand Up @@ -436,7 +436,7 @@ def process_input(metadata_file, country_col, outer_postcode_col, adm1_col, adm2
adm1 = sequence[adm1_col]
outer_postcode = sequence[outer_postcode_col].upper().strip(" ")
adm2 = sequence[adm2_col]
name = sequence["central_sample_id"]
name = sequence[sample_id_col]


if name in fixed_seqs:
Expand Down Expand Up @@ -549,7 +549,7 @@ def process_input(metadata_file, country_col, outer_postcode_col, adm1_col, adm2


if conflict and name not in already_checked_discreps:
incompatible_locations.write(f'{sequence["central_sample_id"]},{outer_postcode},{adm2},{postcode_to_adm2[outer_postcode]},{processed_adm2}\n')
incompatible_locations.write(f'{sequence[sample_id_col]},{outer_postcode},{adm2},{postcode_to_adm2[outer_postcode]},{processed_adm2}\n')
conflict_count += 1

utla = ""
Expand Down Expand Up @@ -634,7 +634,7 @@ def process_input(metadata_file, country_col, outer_postcode_col, adm1_col, adm2

return outer_geog_dict, adm2_to_week_counts, epiweek_dict, non_uk, safe_locs

def make_geography_csv(metadata_file, country_col, outer_postcode_col, adm1_col, adm2_col,epiweek_col, map_utils_dir, outdir):
def make_geography_csv(metadata_file, country_col, outer_postcode_col, adm1_col, adm2_col,epiweek_col, sample_id_col, map_utils_dir, outdir):

country_list = ["UK", "FALKLAND_ISLANDS", "GIBRALTAR", "JERSEY", "ISLE_OF_MAN", "GUERNSEY"]

Expand All @@ -644,7 +644,7 @@ def make_geography_csv(metadata_file, country_col, outer_postcode_col, adm1_col,
writer = csv.DictWriter(fw, fieldnames=fieldnames)
writer.writeheader()

outer_geog_dict, adm2_to_week_counts, epiweek_dict, non_uk, safe_locs = process_input(metadata_file, country_col, outer_postcode_col, adm1_col, adm2_col, epiweek_col, map_utils_dir, outdir)
outer_geog_dict, adm2_to_week_counts, epiweek_dict, non_uk, safe_locs = process_input(metadata_file, country_col, outer_postcode_col, adm1_col, adm2_col, epiweek_col, sample_id_col, map_utils_dir, outdir)

for name, geog_dict in outer_geog_dict.items():
if geog_dict["country"].upper().replace(" ","_") in country_list:
Expand Down Expand Up @@ -702,13 +702,14 @@ def main():
parser.add_argument("--adm2-col", dest="adm2_col")
parser.add_argument("--adm1-col", dest="adm1_col")
parser.add_argument("--epiweek-col", dest="epiweek_col")
parser.add_argument("--sample-id-col", default="central_sample_id")
parser.add_argument("--mapping-utils-dir", dest="map_utils_dir", help="path to map utils eg outer postcode")
parser.add_argument("--outdir")


args = parser.parse_args()

make_geography_csv(args.metadata, args.country_col, args.outer_postcode_col, args.adm1_col, args.adm2_col, args.epiweek_col, args.map_utils_dir, args.outdir)
make_geography_csv(args.metadata, args.country_col, args.outer_postcode_col, args.adm1_col, args.adm2_col, args.epiweek_col, args.sample_id_col, args.map_utils_dir, args.outdir)


if __name__ == '__main__':
Expand Down