import json
import warnings
import pandas as pd
from immuneML.IO.dataset_import.DataImport import DataImport
from immuneML.IO.dataset_import.DatasetImportParams import DatasetImportParams
from immuneML.data_model.dataset.Dataset import Dataset
from immuneML.data_model.receptor.ChainPair import ChainPair
from immuneML.data_model.receptor.RegionType import RegionType
from immuneML.data_model.receptor.receptor_sequence.SequenceFrameType import SequenceFrameType
from immuneML.data_model.repertoire.Repertoire import Repertoire
from immuneML.util.ImportHelper import ImportHelper
from scripts.specification_util import update_docs_per_mapping
[docs]
class VDJdbImport(DataImport):
"""
Imports data in VDJdb format into a Repertoire-, Sequence- or ReceptorDataset.
RepertoireDatasets should be used when making predictions per repertoire, such as predicting a disease state.
SequenceDatasets or ReceptorDatasets should be used when predicting values for unpaired (single-chain) and paired
immune receptors respectively, like antigen specificity.
Arguments:
path (str): For RepertoireDatasets, this is the path to a directory with VDJdb files to import. For Sequence- or ReceptorDatasets this path may either be the path to the file to import, or the path to the folder locating one or multiple files with .tsv, .csv or .txt extensions. By default path is set to the current working directory.
is_repertoire (bool): If True, this imports a RepertoireDataset. If False, it imports a SequenceDataset or ReceptorDataset. By default, is_repertoire is set to True.
metadata_file (str): Required for RepertoireDatasets. This parameter specifies the path to the metadata file. This is a csv file with columns filename, subject_id and arbitrary other columns which can be used as labels in instructions. For setting Sequence- or ReceptorDataset metadata, metadata_file is ignored, see metadata_column_mapping instead.
paired (str): Required for Sequence- or ReceptorDatasets. This parameter determines whether to import a SequenceDataset (paired = False) or a ReceptorDataset (paired = True). In a ReceptorDataset, two sequences with chain types specified by receptor_chains are paired together based on the identifier given in the VDJdb column named 'complex.id'.
receptor_chains (str): Required for ReceptorDatasets. Determines which pair of chains to import for each Receptor. Valid values for receptor_chains are the names of the :py:obj:`~immuneML.data_model.receptor.ChainPair.ChainPair` enum. If receptor_chains is not provided, the chain pair is automatically detected (only one chain pair type allowed per repertoire).
import_illegal_characters (bool): Whether to import sequences that contain illegal characters, i.e., characters that do not appear in the sequence alphabet (amino acids including stop codon '*', or nucleotides). When set to false, filtering is only applied to the sequence type of interest (when running immuneML in amino acid mode, only entries with illegal characters in the amino acid sequence are removed). By default import_illegal_characters is False.
import_empty_nt_sequences (bool): imports sequences which have an empty nucleotide sequence field; can be True or False. By default, import_empty_nt_sequences is set to True.
import_empty_aa_sequences (bool): imports sequences which have an empty amino acid sequence field; can be True or False; for analysis on amino acid sequences, this parameter should be False (import only non-empty amino acid sequences). By default, import_empty_aa_sequences is set to False.
region_type (str): Which part of the sequence to import. By default, this value is set to IMGT_CDR3. This means the first and last amino acids are removed from the CDR3 sequence, as VDJdb uses IMGT junction as CDR3. Specifying any other value will result in importing the sequences as they are. Valid values for region_type are the names of the :py:obj:`~immuneML.data_model.receptor.RegionType.RegionType` enum.
column_mapping (dict): A mapping from VDJdb column names to immuneML's internal data representation. A custom column mapping can be specified here if necessary (for example; adding additional data fields if they are present in the VDJdb file, or using alternative column names). Valid immuneML fields that can be specified here are defined by Repertoire.FIELDS. For VDJdb, this is by default set to:
.. indent with spaces
.. code-block:: yaml
V: v_alleles
J: j_alleles
CDR3: sequence_aas
complex.id: sequence_identifiers
Gene: chains
column_mapping_synonyms (dict): This is a column mapping that can be used if a column could have alternative names. The formatting is the same as column_mapping. If some columns specified in column_mapping are not found in the file, the columns specified in column_mapping_synonyms are instead attempted to be loaded. For VDJdb format, there is no default column_mapping_synonyms.
metadata_column_mapping (dict): Specifies metadata for Sequence- and ReceptorDatasets. This should specify a mapping similar to column_mapping where keys are VDJdb column names and values are the names that are internally used in immuneML as metadata fields. This means that epitope, epitope_gene and epitope_species can be used as prediction labels for Sequence- and ReceptorDatasets. This parameter can also be used to specify sequence-level metadata columns for RepertoireDatasets, which can be used by reports. To set prediction label metadata for RepertoireDatasets, see metadata_file instead. For VDJdb format, this parameter is by default set to:
.. indent with spaces
.. code-block:: yaml
Epitope: epitope
Epitope gene: epitope_gene
Epitope species: epitope_species
separator (str): Column separator, for VDJdb this is by default "\\t".
YAML specification:
.. indent with spaces
.. code-block:: yaml
my_vdjdb_dataset:
format: VDJdb
params:
path: path/to/files/
is_repertoire: True # whether to import a RepertoireDataset
metadata_file: path/to/metadata.csv # metadata file for RepertoireDataset
paired: False # whether to import SequenceDataset (False) or ReceptorDataset (True) when is_repertoire = False
receptor_chains: TRA_TRB # what chain pair to import for a ReceptorDataset
import_illegal_characters: False # remove sequences with illegal characters for the sequence_type being used
import_empty_nt_sequences: True # keep sequences even though the nucleotide sequence might be empty
import_empty_aa_sequences: False # filter out sequences if they don't have sequence_aa set
# Optional fields with VDJdb-specific defaults, only change when different behavior is required:
separator: "\\t" # column separator
region_type: IMGT_CDR3 # what part of the sequence to import
column_mapping: # column mapping VDJdb: immuneML
V: v_genes
J: j_genes
CDR3: sequence_aas
complex.id: sequence_identifiers
Gene: chains
metadata_column_mapping: # metadata column mapping VDJdb: immuneML
Epitope: epitope
Epitope gene: epitope_gene
Epitope species: epitope_species
"""
KEY_MAPPING = {
"subject.id": "subject_id"
}
[docs]
@staticmethod
def import_dataset(params: dict, dataset_name: str) -> Dataset:
return ImportHelper.import_dataset(VDJdbImport, params, dataset_name)
[docs]
@staticmethod
def preprocess_dataframe(df: pd.DataFrame, params: DatasetImportParams):
df["frame_types"] = SequenceFrameType.IN.name
ImportHelper.junction_to_cdr3(df, params.region_type)
df.loc[:, "region_types"] = params.region_type.name
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
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, params.import_with_stop_codon)
ImportHelper.update_gene_info(df)
ImportHelper.load_chains(df)
df["receptor_identifiers"] = df["sequence_identifiers"]
df["sequence_identifiers"] = VDJdbImport.get_sequence_identifiers(df["sequence_identifiers"], df["chains"])
df = VDJdbImport.extract_meta_columns(df, params)
return df
[docs]
@staticmethod
def get_sequence_identifiers(receptor_identifiers, chains):
sequence_identifiers = receptor_identifiers + "_" + chains
if sequence_identifiers.is_unique:
return sequence_identifiers
else:
counts = sequence_identifiers.value_counts()
for id, count in counts[counts > 1].items():
unique_ids = [f"{id}{i}" for i in range(1, count+1)]
sequence_identifiers.loc[sequence_identifiers == id] = unique_ids
return sequence_identifiers
[docs]
@staticmethod
def import_receptors(df, params):
return ImportHelper.import_receptors(df, params)
[docs]
@staticmethod
def get_documentation():
doc = str(VDJdbImport.__doc__)
chain_pair_values = str([chain_pair.name for chain_pair in ChainPair])[1:-1].replace("'", "`")
region_type_values = str([region_type.name for region_type in RegionType])[1:-1].replace("'", "`")
repertoire_fields = list(Repertoire.FIELDS)
repertoire_fields.remove("region_types")
mapping = {
"Valid values for receptor_chains are the names of the :py:obj:`~immuneML.data_model.receptor.ChainPair.ChainPair` enum.": f"Valid values are {chain_pair_values}.",
"Valid values for region_type are the names of the :py:obj:`~immuneML.data_model.receptor.RegionType.RegionType` enum.": f"Valid values are {region_type_values}.",
"Valid immuneML fields that can be specified here are defined by Repertoire.FIELDS": f"Valid immuneML fields that can be specified here are {repertoire_fields}."
}
doc = update_docs_per_mapping(doc, mapping)
return doc