Python interface to LinearPartition, a linear-time RNA secondary structure prediction tool
Project description
python-linearpartition
Unofficial CPython binding to LinearPartition
Installation
Use pip
to install the module.
pip install linearpartition-unofficial
You may build from the source code for unsupported Python versions or platforms.
git clone --recursive https://github.com/ChangLabSNU/python-linearpartition
cd python-linearpartition
pip install .
Usage
The module currently only has one function called partition(seq)
, and
it doesn't have any customizable options other than the defaults.
The seq parameter should be an RNA sequence in uppercase letters,
and any T
should be converted to U
before passing it to the function.
>>> import linearpartition as lp
>>> seq = 'UGUCGGGGUUGGCUGUCUGACA'
>>> bpmtx, fe = lp.partition(seq)
>>> fe
-7.216465644007023
>>> import pandas as pd
>>> pd.DataFrame(bpmtx).sort_values('prob', ascending=False).head()
i j prob
19 3 18 0.999201
18 2 19 0.998801
17 1 20 0.997717
21 5 16 0.996692
22 4 17 0.996508
The function returns a tuple with two elements. The first element is the predicted base pairing probability, and the second element is the free energy of the ensemble structure in kcal/mol.
Author
Hyeshik Chang <hyeshik@snu.ac.kr>
License
This Python binding is licensed under the MIT-style license. However, the compiled binary includes code from the LinearPartition package, which is licensed for non-commercial use.
Project details
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