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import functools |
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import typing as ty |
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import pandas as pd |
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import RNA |
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@functools.lru_cache() |
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def duplex_energy(s1: str, s2: str) -> float: |
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return RNA.duplexfold(s1, s2).energy |
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@functools.lru_cache() |
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def folded_sequence(sequence, model_details): |
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folder = RNA.fold_compound(sequence, model_details) |
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dot_bracket, mfe = folder.mfe() |
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return dot_bracket, mfe |
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def fold_sequences( |
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sequences: ty.Iterable[str], temperature: float = 37.0, |
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) -> pd.DataFrame: |
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md = RNA.md() |
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md.temperature = temperature |
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seq2structure_map = { |
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"sequence": [], |
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f"structure_{int(temperature)}": [], |
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f"mfe_{int(temperature)}": [], |
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} |
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for sequence in sequences: |
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dot_bracket, mfe = folded_sequence(sequence, md) |
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seq2structure_map["sequence"].append(sequence) |
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seq2structure_map[f"structure_{int(temperature)}"].append(dot_bracket) |
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seq2structure_map[f"mfe_{int(temperature)}"].append(mfe) |
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return pd.DataFrame(seq2structure_map).set_index("sequence") |
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def fraction(seq: str, nucleoids: str) -> float: |
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"""Computes the fraction of the sequence string that is the set of nucleoids |
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given. |
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Parameters |
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---------- |
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seq : str |
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The sequence string |
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nucleoids : str |
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The list of nucleoids to compute the fraction for. |
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Returns |
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------- |
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float |
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The fraction |
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""" |
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return sum([seq.count(n) for n in nucleoids]) / len(seq) |
