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"""Paired sequences from the Observed Antibody Space database""" |
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import datasets |
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import pandas as pd |
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import os |
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_CITATION = """\ |
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@article{Olsen_Boyles_Deane_2022, |
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title={Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences}, |
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volume={31}, rights={© 2021 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.}, |
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ISSN={1469-896X}, DOI={10.1002/pro.4205}, |
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number={1}, journal={Protein Science}, author={Olsen, Tobias H. and Boyles, Fergus and Deane, Charlotte M.}, |
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year={2022}, pages={141–146}, language={en} } |
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""" |
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_DESCRIPTION = """\ |
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Paired heavy and light chain antibody sequences for multiple species. |
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""" |
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_HOMEPAGE = "https://opig.stats.ox.ac.uk/webapps/oas/" |
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_LICENSE = "cc-by-4.0" |
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_BASE_URL = "https://aws-hcls-ml.s3.amazonaws.com/oas-paired-sequence-data/parquet/" |
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_URLS = { |
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"human": _BASE_URL + "human.tar.gz", |
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"rat_SD": _BASE_URL + "rat_SD.tar.gz", |
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"mouse_BALB_c": _BASE_URL + "mouse_BALB_c.tar.gz", |
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"mouse_C57BL_6": _BASE_URL + "mouse_C57BL_6.tar.gz", |
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} |
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_FEATURES = datasets.Features( |
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{ |
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"sequence_alignment_aa_heavy": datasets.Value("string"), |
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"cdr1_aa_heavy": datasets.Value("string"), |
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"cdr2_aa_heavy": datasets.Value("string"), |
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"cdr3_aa_heavy": datasets.Value("string"), |
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"sequence_alignment_aa_light": datasets.Value("string"), |
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"cdr1_aa_light": datasets.Value("string"), |
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"cdr2_aa_light": datasets.Value("string"), |
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"cdr3_aa_light": datasets.Value("string"), |
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} |
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) |
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class OasPairedSequenceData(datasets.GeneratorBasedBuilder): |
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"""OAS paired sequence data.""" |
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VERSION = datasets.Version("1.2.0") |
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BUILDER_CONFIGS = [ |
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datasets.BuilderConfig(name="human", version=VERSION, description="human"), |
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datasets.BuilderConfig(name="rat_SD", version=VERSION, description="rat_SD"), |
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datasets.BuilderConfig( |
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name="mouse_BALB_c", version=VERSION, description="mouse_BALB_c" |
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), |
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datasets.BuilderConfig( |
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name="mouse_C57BL_6", version=VERSION, description="mouse_C57BL_6" |
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), |
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] |
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def _info(self): |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=_FEATURES, |
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homepage=_HOMEPAGE, |
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license=_LICENSE, |
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citation=_CITATION, |
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) |
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def _split_generators(self, dl_manager): |
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urls = _URLS[self.config.name] |
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data_dir = dl_manager.download_and_extract(urls) |
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return [ |
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datasets.SplitGenerator( |
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name=datasets.Split.TRAIN, |
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gen_kwargs={ |
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"filepath": os.path.join(data_dir), |
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"split": "train", |
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}, |
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), |
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] |
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def _generate_examples(self, filepath, split): |
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table = pd.read_parquet(filepath) |
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for key, row in enumerate(table.itertuples()): |
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if key == 0: |
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continue |
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yield key, { |
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"sequence_alignment_aa_heavy": row[1], |
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"cdr1_aa_heavy": row[2], |
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"cdr2_aa_heavy": row[3], |
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"cdr3_aa_heavy": row[4], |
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"sequence_alignment_aa_light": row[5], |
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"cdr1_aa_light": row[6], |
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"cdr2_aa_light": row[7], |
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"cdr3_aa_light": row[8], |
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} |
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