def _repertoire_to_dataframe(repertoire: Repertoire, region_type):
# get all fields (including custom fields)
df = pd.DataFrame(repertoire.load_data())
for column in ['v_alleles', 'j_alleles', 'v_genes', 'j_genes']:
if column not in df.columns:
df.loc[:, column] = None
AIRRExporter.update_gene_columns(df, 'alleles', 'genes')
# rename mandatory fields for airr-compliance
mapper = {"sequence_identifiers": "sequence_id", "v_alleles": "v_call", "j_alleles": "j_call", "chains": "locus", "counts": "duplicate_count",
"sequences": AIRRExporter.get_sequence_field(region_type), "sequence_aas": AIRRExporter.get_sequence_aa_field(region_type)}
df = df.rename(mapper=mapper, axis="columns")
return df
def process_repertoire(repertoire: Repertoire, params: dict) -> Repertoire:
data = pd.DataFrame(repertoire.load_data())
groupby_fields = DuplicateSequenceFilter._prepare_group_by_field(
params, data.columns)
custom_lists = list(set(data.columns) - set(Repertoire.FIELDS))
agg_dict = DuplicateSequenceFilter._prepare_agg_dict(
params, data.columns, custom_lists)
# Chain objects can not be aggregated, convert to strings
if "chains" in data.columns:
data["chains"] = [
chain.value if isinstance(chain, Chain) else chain
for chain in data["chains"]
]
else:
data["chains"] = None
no_duplicates = data.groupby(groupby_fields).agg(
agg_dict).reset_index()
processed_repertoire = Repertoire.build(
sequence_aas=list(no_duplicates["sequence_aas"])
if "sequence_aas" in no_duplicates.columns else None,
sequences=list(no_duplicates["sequences"])
if "sequences" in no_duplicates.columns else None,
v_genes=list(no_duplicates["v_genes"])
if "v_genes" in no_duplicates.columns else None,
j_genes=list(no_duplicates["j_genes"])
if 'j_genes' in no_duplicates.columns else None,
chains=[Chain(key) for key in list(no_duplicates["chains"])]
if "chains" in no_duplicates.columns else None,
counts=list(no_duplicates["counts"])
if "counts" in no_duplicates else None,
region_types=list(no_duplicates["region_types"])
if "region_types" in no_duplicates else None,
custom_lists={
key: list(no_duplicates[key])
for key in custom_lists
},
sequence_identifiers=list(no_duplicates["sequence_identifiers"]),
metadata=copy.deepcopy(repertoire.metadata),
path=params["result_path"])
return processed_repertoire