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