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| |
| |
| """Paired sequences from the Observed Antibody Space database""" |
| import csv |
| import datasets |
| import os |
|
|
| _CITATION = """\ |
| @article{Olsen_Boyles_Deane_2022, |
| title={Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences}, |
| volume={31}, rights={© 2021 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.}, |
| ISSN={1469-896X}, DOI={10.1002/pro.4205}, |
| number={1}, journal={Protein Science}, author={Olsen, Tobias H. and Boyles, Fergus and Deane, Charlotte M.}, |
| year={2022}, pages={141–146}, language={en} } |
| |
| """ |
| _DESCRIPTION = """\ |
| Paired heavy and light chain antibody sequences for multiple species. |
| """ |
|
|
| _HOMEPAGE = "https://opig.stats.ox.ac.uk/webapps/oas/" |
|
|
| _LICENSE = "cc-by-4.0" |
|
|
| _BASE_URL = "https://aws-hcls-ml.s3.amazonaws.com/oas-paired-sequence-data/" |
| _URLS = { |
| "human": _BASE_URL + "human.zip", |
| "rat_SD": _BASE_URL + "rat_SD.zip", |
| "mouse_BALB_c": _BASE_URL + "mouse_BALB_c.zip", |
| "mouse_C57BL_6": _BASE_URL + "mouse_C57BL_6.zip", |
| } |
|
|
| _FEATURES = datasets.Features( |
| { |
| "pair_id": datasets.Value("string"), |
| "sequence_alignment_aa_heavy": datasets.Value("string"), |
| "sequence_alignment_aa_light": datasets.Value("string"), |
| "cdr1_aa_heavy_start": datasets.Value("int16"), |
| "cdr1_aa_heavy_end": datasets.Value("int16"), |
| "cdr1_aa_light_start": datasets.Value("int16"), |
| "cdr1_aa_light_end": datasets.Value("int16"), |
| "cdr2_aa_heavy_start": datasets.Value("int16"), |
| "cdr2_aa_heavy_end": datasets.Value("int16"), |
| "cdr2_aa_light_start": datasets.Value("int16"), |
| "cdr2_aa_light_end": datasets.Value("int16"), |
| "cdr3_aa_heavy_start": datasets.Value("int16"), |
| "cdr3_aa_heavy_end": datasets.Value("int16"), |
| "cdr3_aa_light_start": datasets.Value("int16"), |
| "cdr3_aa_light_end": datasets.Value("int16"), |
| } |
| ) |
|
|
|
|
| class OasPairedSequenceData(datasets.GeneratorBasedBuilder): |
| """OAS paired sequence data.""" |
|
|
| VERSION = datasets.Version("1.1.0") |
| BUILDER_CONFIGS = [ |
| datasets.BuilderConfig(name="human", version=VERSION, description="Human"), |
| datasets.BuilderConfig(name="rat_SD", version=VERSION, description="rat_SD"), |
| datasets.BuilderConfig( |
| name="mouse_BALB_c", version=VERSION, description="mouse_BALB_c" |
| ), |
| datasets.BuilderConfig( |
| name="mouse_C57BL_6", version=VERSION, description="mouse_C57BL_6" |
| ), |
| ] |
|
|
| def _info(self): |
| return datasets.DatasetInfo( |
| description=_DESCRIPTION, |
| features=_FEATURES, |
| homepage=_HOMEPAGE, |
| license=_LICENSE, |
| citation=_CITATION, |
| ) |
|
|
| def _split_generators(self, dl_manager): |
| urls = _URLS[self.config.name] |
| data_dir = dl_manager.download_and_extract(urls) |
| return [ |
| datasets.SplitGenerator( |
| name=datasets.Split.TRAIN, |
| gen_kwargs={ |
| "filepath": os.path.join(data_dir, "train.csv"), |
| "split": "train", |
| }, |
| ), |
| ] |
|
|
| def _generate_examples(self, filepath, split): |
| with open(filepath, newline="") as f: |
| reader = csv.reader(f, delimiter=",") |
| for key, row in enumerate(reader): |
| if key == 0: |
| continue |
| yield key, { |
| "pair_id": row[0], |
| "sequence_alignment_aa_heavy": row[1], |
| "sequence_alignment_aa_light": row[2], |
| "cdr1_aa_heavy_start": row[3], |
| "cdr1_aa_heavy_end": row[4], |
| "cdr1_aa_light_start": row[5], |
| "cdr1_aa_light_end": row[6], |
| "cdr2_aa_heavy_start": row[7], |
| "cdr2_aa_heavy_end": row[8], |
| "cdr2_aa_light_start": row[9], |
| "cdr2_aa_light_end": row[10], |
| "cdr3_aa_heavy_start": row[11], |
| "cdr3_aa_heavy_end": row[12], |
| "cdr3_aa_light_start": row[13], |
| "cdr3_aa_light_end": row[14], |
| } |
|
|
|
|
