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--- |
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configs: |
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- config_name: full |
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default: true |
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data_files: |
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- split: validation |
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path: valid_full.parquet |
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- config_name: 10k |
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data_files: |
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- split: validation |
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path: valid_10k.parquet |
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--- |
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# Evolutionary constraint prediction |
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## Reproducing this dataset |
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```python |
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import pandas as pd |
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CENTER_POSITION = 255 |
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NUCLEOTIDES = list("ACGT") |
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df = pd.read_csv("hf://datasets/kuleshov-group/cross-species-single-nucleotide-annotation/Evolutionary_constraint/valid.tsv", sep="\t") |
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df = df.rename(columns={"sequences": "seq"}) |
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df["chrom_pos"] = df.pos |
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df["pos"] = CENTER_POSITION |
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df["ref"] = df.seq.str[CENTER_POSITION] |
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def subsample(df, n, seed): |
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return ( |
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df.groupby('label').apply(lambda x: x.sample(n=n // 2, random_state=seed)) |
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.reset_index(drop=True) |
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.sort_values(["chrom", "chrom_pos"]) |
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) |
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df.drop(columns=["ref"]).to_parquet("valid_full.parquet", index=False) |
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subsample(df[df.ref.isin(NUCLEOTIDES)].drop(columns=["ref"]), 10_000, 42).to_parquet("valid_10k.parquet", index=False) |
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``` |
