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Fix pandas warning for rel_dna_ser.txt #145

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Feb 10, 2022
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Fix pandas warning for rel_dna_ser.txt #145

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19 changes: 16 additions & 3 deletions pyard/data_repository.py
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Original file line number Diff line number Diff line change
Expand Up @@ -387,15 +387,28 @@ def to_serological_name(locus_name: str):

def generate_serology_mapping(db_connection: sqlite3.Connection, imgt_version):
if not db.table_exists(db_connection, 'serology_mapping'):
# Load WMDA serology mapping data
"""
Read `rel_dna_ser.txt` file that contains alleles and their serological equivalents.

The fields of the Alleles->Serological mapping file are:
Locus - HLA Locus
Allele - HLA Allele Name
USA - Unambiguous Serological Antigen associated with allele
PSA - Possible Serological Antigen associated with allele
ASA - Assumed Serological Antigen associated with allele
EAE - Expert Assigned Exceptions in search determinants of some registries

EAE is ignored when generating the serology map.
"""
rel_dna_ser_url = f'{IMGT_HLA_URL}{imgt_version}/wmda/rel_dna_ser.txt'
# Load WMDA serology mapping data from URL
df_sero = pd.read_csv(rel_dna_ser_url, sep=';', skiprows=6,
names=['Locus', 'Allele', 'USA', 'PSA', 'ASA'],
names=['Locus', 'Allele', 'USA', 'PSA', 'ASA', 'EAE'],
index_col=False)

# Remove 0 and ? from USA
df_sero = df_sero[(df_sero['USA'] != '0') & (df_sero['USA'] != '?')]
df_sero['Allele'] = df_sero['Locus'] + df_sero['Allele']
df_sero['Allele'] = df_sero.loc[:, 'Locus'] + df_sero.loc[:, 'Allele']

usa = df_sero[['Locus', 'Allele', 'USA']].dropna()
usa['Sero'] = usa['Locus'] + usa['USA']
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