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import datasets |
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import pandas as pd |
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_CITATION = """\ |
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Feng Q, Liang S, Jia H, et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat Commun. 2015;6:6528. Published 2015 Mar 11. doi:10.1038/ncomms7528 |
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""" |
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_DESCRIPTION = """\ |
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The dataset contains 16S rRNA gene sequencing data from healthy controls and colorectal cancer patients. The dataset was used in the paper "Gut microbiome development along the colorectal adenoma-carcinoma sequence" by Feng et al. (2015). |
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""" |
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_HOMEPAGE = "https://pubmed.ncbi.nlm.nih.gov/25758642/" |
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class ColorectalCarcinomaMicrobiomeFengQConfig(datasets.GeneratorBasedBuilder): |
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BUILDER_CONFIGS = [ |
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datasets.BuilderConfig( |
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name="presence-absence", |
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description="Binary presence/absence of taxa", |
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), |
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datasets.BuilderConfig( |
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name="CLR", |
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description="Relative abundance of taxa", |
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), |
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] |
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DEFAULT_CONFIG_NAME = "presence-absence" |
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def _info(self): |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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citation=_CITATION, |
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homepage=_HOMEPAGE, |
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version=datasets.Version("0.1.0"), |
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) |
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def _split_generators(self, dl_manager): |
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if self.config.name == "presence-absence": |
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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": "PA_train.csv", |
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"split": "train", |
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}, |
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), |
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datasets.SplitGenerator( |
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name=datasets.Split.TEST, |
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gen_kwargs={ |
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"filepath": "PA_test.csv", |
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"split": "test", |
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}, |
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), |
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] |
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elif self.config.name == "CLR": |
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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": "CLR_train.csv", |
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}, |
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), |
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datasets.SplitGenerator( |
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name=datasets.Split.TEST, |
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gen_kwargs={ |
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"filepath": "CLR_test.csv", |
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}, |
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), |
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] |
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def _generate_examples(self, filepath, split=None): |
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df = pd.read_csv(filepath) |
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for i, row in df.iterrows(): |
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target = row["target"] |
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values = row.drop("target").values |
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yield i, { |
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"values": values, |
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"target": target, |
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} |
