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#!/usr/bin/env python
# coding=utf-8
# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: MIT-0
"""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/processed/"
_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"),
"cdr1_aa_heavy": datasets.Value("string"),
"cdr2_aa_heavy": datasets.Value("string"),
"cdr3_aa_heavy": datasets.Value("string"),
"sequence_alignment_aa_light": datasets.Value("string"),
"cdr1_aa_light": datasets.Value("string"),
"cdr2_aa_light": datasets.Value("string"),
"cdr3_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("1.2.0")
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, encoding="utf-8", 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],
"cdr1_aa_heavy": row[2],
"cdr2_aa_heavy": row[3],
"cdr3_aa_heavy": row[4],
"sequence_alignment_aa_light": row[5],
"cdr1_aa_light": row[6],
"cdr2_aa_light": row[7],
"cdr3_aa_light": row[8],
# "cdr1_aa_heavy_start": row[9],
# "cdr1_aa_heavy_end": row[10],
# "cdr1_aa_light_start": row[11],
# "cdr1_aa_light_end": row[12],
# "cdr2_aa_heavy_start": row[13],
# "cdr2_aa_heavy_end": row[14],
# "cdr2_aa_light_start": row[15],
# "cdr2_aa_light_end": row[16],
# "cdr3_aa_heavy_start": row[17],
# "cdr3_aa_heavy_end": row[18],
# "cdr3_aa_light_start": row[19],
# "cdr3_aa_light_end": row[20],
}
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