def preprocess_dataframe(df: pd.DataFrame, params):
subframes = []
chain_dups_to_process = ("1", "2") if params.import_dual_chains is True else ("1")
for chain in params.receptor_chains.value:
for chain_dup in chain_dups_to_process:
subframe_dict = {"cell_ids": df["Clonotype ID"],
"sequence_aas": df[f"Chain: {chain} ({chain_dup})"],
"v_genes": df[f"{chain} - V gene ({chain_dup})"],
"j_genes": df[f"{chain} - J gene ({chain_dup})"],
"chains": Chain.get_chain(chain).value}
if params.extra_columns_to_load is not None:
for extra_col in params.extra_columns_to_load:
subframe_dict[extra_col] = df[extra_col]
subframes.append(pd.DataFrame(subframe_dict))
df = pd.concat(subframes, axis=0)
df.dropna(subset=["sequence_aas", "v_genes", "j_genes"], inplace=True)
df.reset_index(drop=True, inplace=True)
if params.import_all_gene_combinations:
df = IRISImport.import_all_gene_combinations(df)
else:
for gene_column in ("v_genes", "j_genes"):
processed_names = [IRISImport._load_gene(rn.choice(raw_v_string.split(" | "))) for raw_v_string in df[gene_column]]
df[gene_column] = processed_names
ImportHelper.drop_empty_sequences(df, params.import_empty_aa_sequences, params.import_empty_nt_sequences)
return df
def preprocess_dataframe(dataframe: pd.DataFrame, params: DatasetImportParams):
dataframe.loc[:, "frame_types"] = dataframe.frame_types.str.upper()
frame_type_list = ImportHelper.prepare_frame_type_list(params)
dataframe = dataframe[dataframe["frame_types"].isin(frame_type_list)]
dataframe.loc[:, "region_types"] = params.region_type.name
if params.region_type == RegionType.IMGT_CDR3:
if "sequences" in dataframe.columns:
dataframe.loc[:, 'sequences'] = [y[(84 - 3 * len(x)): 78] if x is not None else None for x, y in zip(dataframe['sequence_aas'], dataframe['sequences'])]
dataframe.loc[:, 'sequence_aas'] = dataframe["sequence_aas"].str[1:-1]
elif "sequences" in dataframe.columns:
dataframe.loc[:, 'sequences'] = [y[(81 - 3 * len(x)): 81] if x is not None else None for x, y in zip(dataframe['sequence_aas'], dataframe['sequences'])]
dataframe = AdaptiveImportHelper.parse_adaptive_germline_to_imgt(dataframe, params.organism)
dataframe = ImportHelper.standardize_none_values(dataframe)
ImportHelper.drop_empty_sequences(dataframe, params.import_empty_aa_sequences, params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(dataframe, params.import_illegal_characters)
if "chains" in dataframe.columns:
dataframe.loc[:, "chains"] = ImportHelper.load_chains(dataframe)
else:
# loading from v_subgroups is preferred as sometimes v_genes is None when v_subgroups is defined
if "v_subgroups" in dataframe.columns:
dataframe.loc[:, "chains"] = ImportHelper.load_chains_from_column(dataframe, "v_subgroups")
else:
dataframe.loc[:, "chains"] = ImportHelper.load_chains_from_genes(dataframe)
return dataframe
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
df["frame_types"] = SequenceFrameType.IN.name
ImportHelper.junction_to_cdr3(df, params.region_type)
if not params.is_repertoire and params.paired:
n_single_chains = sum(df["sequence_identifiers"] == "0")
if n_single_chains > 0:
df.drop(df.loc[df["sequence_identifiers"] == "0"].index, inplace=True)
warnings.warn(f"VDJdbImport: {n_single_chains} single chains were removed when trying to create a ReceptorDataset.\n"
f"To import all chains as a SequenceDataset, use paired = False")
else:
df.loc[df["sequence_identifiers"] == "0", "sequence_identifiers"] = None
if "chains" not in df.columns:
df.loc[:, "chains"] = ImportHelper.load_chains_from_genes(df)
df["receptor_identifiers"] = df["sequence_identifiers"]
df["sequence_identifiers"] = VDJdbImport.get_sequence_identifiers(df["sequence_identifiers"], df["chains"])
ImportHelper.update_gene_info(df)
ImportHelper.drop_empty_sequences(df, params.import_empty_aa_sequences, params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(df, params.import_illegal_characters)
df = VDJdbImport.extract_meta_columns(df, params)
return df
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
ImportHelper.junction_to_cdr3(df, params.region_type)
ImportHelper.drop_empty_sequences(df, params.import_empty_aa_sequences,
params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(
df, params.import_illegal_characters)
ImportHelper.update_gene_info(df)
return df
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
"""
Function for preprocessing data from a dataframe containing AIRR data, such that:
- productive sequences, sequences with stop codons or out of frame sequences are filtered according to specification
- if RegionType is CDR3, the leading C and trailing W are removed from the sequence to match the CDR3 definition
- if no chain column was specified, the chain is extracted from the v gene name
- the allele information is removed from the V and J genes
"""
if "productive" in df.columns:
df["frame_types"] = SequenceFrameType.OUT.name
df.loc[df["productive"] == True,
"frame_types"] = SequenceFrameType.IN.name
else:
df["frame_types"] = None
if "vj_in_frame" in df.columns:
df.loc[df["vj_in_frame"] == True,
"frame_types"] = SequenceFrameType.IN.name
if "stop_codon" in df.columns:
df.loc[df["stop_codon"] == True,
"frame_types"] = SequenceFrameType.STOP.name
if "productive" in df.columns:
frame_type_list = ImportHelper.prepare_frame_type_list(params)
df = df[df["frame_types"].isin(frame_type_list)]
if params.region_type == RegionType.IMGT_CDR3:
if "sequence_aas" not in df.columns and "sequences" not in df.columns:
if "cdr3" in df.columns:
df.rename(columns={"cdr3": "sequences"}, inplace=True)
if "cdr3_aa" in df.columns:
df.rename(columns={"cdr3_aa": "sequence_aas"},
inplace=True)
df.loc[:, "region_types"] = params.region_type.name
elif "junction" in params.column_mapping or "junction_aa" in params.column_mapping:
ImportHelper.junction_to_cdr3(df, params.region_type)
# todo else: support "full_sequence" import through regiontype?
if "chains" not in df.columns:
df.loc[:, "chains"] = ImportHelper.load_chains_from_genes(df)
df = ImportHelper.update_gene_info(df)
ImportHelper.drop_empty_sequences(df, params.import_empty_aa_sequences,
params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(
df, params.import_illegal_characters)
return df
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
if "sequences" not in df.columns and "sequence_aas" not in df.columns:
raise IOError(
"OLGAImport: Columns should contain at least 'sequences' or 'sequence_aas'."
)
if "counts" not in df.columns:
df["counts"] = 1
df["sequence_identifiers"] = None
ImportHelper.junction_to_cdr3(df, params.region_type)
ImportHelper.drop_empty_sequences(df, params.import_empty_aa_sequences,
params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(
df, params.import_illegal_characters)
if "chains" not in df.columns:
df.loc[:, "chains"] = ImportHelper.load_chains_from_genes(df)
return df
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
if "counts" not in df.columns:
df["counts"] = 1
df = df[df.anchors_found == "1"]
if not params.import_out_of_frame:
df = df[df.is_inframe == "1"]
df["sequence_aas"] = df["sequences"].apply(IGoRImport.translate_sequence)
if not params.import_with_stop_codon:
no_stop_codon = ["*" not in seq for seq in df.sequence_aas]
df = df[no_stop_codon]
ImportHelper.junction_to_cdr3(df, params.region_type)
# note: import_empty_aa_sequences is set to true here; since IGoR doesnt output aa, this parameter is insensible
ImportHelper.drop_empty_sequences(df, True, params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(df, params.import_illegal_characters)
# chain or at least receptorsequence?
return df
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
"""
Function for loading the data from one MiXCR file, such that:
- for the given region (CDR3/full sequence), both nucleotide and amino acid sequence are loaded
- if the region is CDR3, it adapts the sequence to the definition of the CDR3 (IMGT junction vs IMGT CDR3)
- the chain for each sequence is extracted from the v gene name
- the genes are loaded from the top score for gene without allele info
Arguments:
metadata: the corresponding row from the metadata file with metadata such as subject_id, age, HLA or other info given there
params: DatasetImportParams object defining what to import and how to do it
Returns:
data frame corresponding to Repertoire.FIELDS and custom lists which can be used to create a Repertoire object
"""
df["sequence_aas"] = df[MiXCRImport.SEQUENCE_NAME_MAP[
params.region_type]["AA"]]
df["sequences"] = df[MiXCRImport.SEQUENCE_NAME_MAP[params.region_type]
["NT"]]
ImportHelper.junction_to_cdr3(df, params.region_type)
df["counts"] = df["counts"].astype(float).astype(int)
df["v_genes"] = MiXCRImport._load_genes(df, "v_genes")
df["j_genes"] = MiXCRImport._load_genes(df, "j_genes")
df["chains"] = ImportHelper.load_chains_from_genes(df)
ImportHelper.update_gene_info(df)
ImportHelper.drop_empty_sequences(df, params.import_empty_aa_sequences,
params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(
df, params.import_illegal_characters)
return df
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
df["frame_types"] = None
df.loc[df["productive"].eq("True"),
"frame_types"] = SequenceFrameType.IN.name
allowed_productive_values = []
if params.import_productive:
allowed_productive_values.append("True")
if params.import_unproductive:
allowed_productive_values.append("False")
df = df[df.productive.isin(allowed_productive_values)]
ImportHelper.junction_to_cdr3(df, params.region_type)
ImportHelper.drop_empty_sequences(df, params.import_empty_aa_sequences,
params.import_empty_nt_sequences)
ImportHelper.drop_illegal_character_sequences(
df, params.import_illegal_characters)
ImportHelper.update_gene_info(df)
if "chains" not in df.columns:
df.loc[:, "chains"] = ImportHelper.load_chains_from_genes(df)
return df
