用于MaxEntScan的Python包装器，用于计算拼接位点强.zip

# maxentpy [](https://github.com/kepbod/maxentpy/actions?query=workflow%3ABuild) [](https://coveralls.io/github/kepbod/maxentpy) [](http://bioconda.github.io/recipes/maxentpy/README.html) [](https://anaconda.org/bioconda/maxentpy) maxentpy is a python wrapper for MaxEntScan to calculate splice site strength. It contains two functions. `score5` is adapt from [MaxEntScan::score5ss](http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html) to score 5' splice sites. `score3` is adapt from [MaxEntScan::score3ss](http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq_acc.html) to score 3' splice sites. They only use Maximum Entropy Model to score. ## Prerequisites * Cython * msgpack-python ## Examples ```python >>> from maxentpy import maxent # use normal version of maxent >>> maxent.score5('cagGTAAGT') # 3 bases in exon and 6 bases in intron 10.858313101356437 >>> maxent.score3('ttccaaacgaacttttgtAGgga') # 20 bases in the intron and 3 base in the exon 2.8867730651152104 >>> from maxentpy.maxent import load_matrix5, load_matrix3 # preloading matrix will speed up >>> timeit maxent.score5('cagGTAAGT') 10 loops, best of 3: 23.5 ms per loop >>> matrix5 = load_matrix5() >>> timeit maxent.score5('cagGTAAGT', matrix=matrix5) 100000 loops, best of 3: 3.27 µs per loop >>> timeit maxent.score3('ttccaaacgaacttttgtAGgga') 1 loop, best of 3: 259 ms per loop >>> matrix3 = load_matrix3() >>> timeit maxent.score3('ttccaaacgaacttttgtAGgga', matrix=matrix3) 10000 loops, best of 3: 103 µs per loop >>> from maxentpy import maxent_fast # fast version could further speed up >>> timeit maxent_fast.score5('cagGTAAGT') 100 loops, best of 3: 5.04 ms per loop >>> timeit maxent_fast.score3('ttccaaacgaacttttgtAGgga') 100 loops, best of 3: 9.3 ms per loop >>> from maxentpy.maxent_fast import load_matrix # support preloading matrix >>> matrix5 = load_matrix(5) >>> timeit maxent_fast.score5('cagGTAAGT', matrix=matrix5) 100000 loops, best of 3: 3.61 µs per loop >>> matrix3 = load_matrix(3) >>> timeit maxent_fast.score3('ttccaaacgaacttttgtAGgga', matrix=matrix3) 100000 loops, best of 3: 7.76 µs per loop ``` ## Benchmark ### score5 score5 |maxentpy.maxent|maxentpy.maxent_fast --------------|---------------|-------------------- without matrix| 23.5 ms | 5.04 ms with matrix | 3.27 µs | 3.61 µs ### score3 score3 |maxentpy.maxent|maxentpy.maxent_fast --------------|---------------|-------------------- without matrix| 259 ms | 9.3 ms with matrix | 103 µs | 7.76 µs ## Citation Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. Journal of Computational Biology. 2004, 11:377-94. ## License The original algorithm and perl scripts are under license described in http://genes.mit.edu/burgelab/maxent/download/READTHIS. The python version of maxent is under the [MIT License](https://opensource.org/licenses/MIT).