msasim 2024.5.22__cp312-cp312-macosx_11_0_arm64.whl → 2024.5.221251__cp312-cp312-macosx_11_0_arm64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- msasim-2024.5.221251.dist-info/METADATA +54 -0
- msasim-2024.5.221251.dist-info/RECORD +8 -0
- {msasim-2024.5.22.dist-info → msasim-2024.5.221251.dist-info}/top_level.txt +1 -1
- msasim-2024.5.22.dist-info/METADATA +0 -13
- msasim-2024.5.22.dist-info/RECORD +0 -8
- {Sailfish → msasim}/__init__.py +0 -0
- /Sailfish/simulator.py → /msasim/sailfish.py +0 -0
- {msasim-2024.5.22.dist-info → msasim-2024.5.221251.dist-info}/LICENSE +0 -0
- {msasim-2024.5.22.dist-info → msasim-2024.5.221251.dist-info}/WHEEL +0 -0
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Metadata-Version: 2.1
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Name: msasim
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Version: 2024.5.221251
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Summary: A fast MSA simulator
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Home-page: https://github.com/elyawy/Sailfish-backend
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Author: Elya Wygoda
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Author-email: elya.wygoda@gmail.com
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Requires-Python: >=3.6
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Provides-Extra: test
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Requires-Dist: pytest ; extra == 'test'
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# Sailfish
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Sailfish is a performant multiple sequence alignment(MSA) simulator, written in C++ and Python, allowing for quick and easy generation of large simulated datasets.
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## Project goals
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- Ease of use
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- Speed
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- Modularity
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## Installation
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```bash
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pip install msasim
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```
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## Example
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```python
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from msasim import sailfish as sim
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from msasim.sailfish import MODEL_CODES, ZipfDistribution
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ROOT_SEQUENCE_LENGTH = 100
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sim_protocol = sim.SimProtocol("(A:0.5,B:0.5);",
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deletion_rate=0.01,
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insertion_rate=0.01,
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deletion_dist=ZipfDistribution(1.08, 50),
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insertion_dist=ZipfDistribution(1.08, 50),
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seed=50)
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sim_protocol.set_sequence_size(ROOT_SEQUENCE_LENGTH)
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simulation = sim.Simulator(sim_protocol, simulation_type=sim.SIMULATION_TYPE.PROTEIN)
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simulation.set_replacement_model(model=MODEL_CODES.WAG,
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gamma_parameters_alpha=1.0,
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gamma_parameters_catergories=4)
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msa = simulation()
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msa.print_msa()
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```
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_Sailfish.cpython-312-darwin.so,sha256=Qu8pn_Zynt6onssgqcxnLa0cPgK6-LohNLqtuuTqBKU,1002912
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msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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msasim/sailfish.py,sha256=CTFAnavIHy918aF141FKeZjO5Y-oYASI-TR5MMGGVks,24324
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msasim-2024.5.221251.dist-info/RECORD,,
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msasim-2024.5.221251.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
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msasim-2024.5.221251.dist-info/WHEEL,sha256=Vo9YTsjXxZ5SWdH4n69oS5jU3YTIi3eHk0n-aUcTtlw,110
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msasim-2024.5.221251.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
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msasim-2024.5.221251.dist-info/METADATA,sha256=gbSrrmjeUV2fvugSXR2i1SOYyZv2k3jKjAqI97sakbM,1474
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Metadata-Version: 2.1
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Name: msasim
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Version: 2024.5.22
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Summary: A fast MSA simulator
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Home-page: https://github.com/elyawy/Sailfish-backend
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Author: Elya Wygoda
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Author-email: elya.wygoda@gmail.com
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Requires-Python: >=3.6
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License-File: LICENSE
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Provides-Extra: test
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Requires-Dist: pytest ; extra == 'test'
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Sailfish is a performant multiple sequence alignment simulator, written in C++, allowing fast generation of large simualted datasets.
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_Sailfish.cpython-312-darwin.so,sha256=Qu8pn_Zynt6onssgqcxnLa0cPgK6-LohNLqtuuTqBKU,1002912
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msasim-2024.5.22.dist-info/RECORD,,
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msasim-2024.5.22.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
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msasim-2024.5.22.dist-info/WHEEL,sha256=Vo9YTsjXxZ5SWdH4n69oS5jU3YTIi3eHk0n-aUcTtlw,110
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msasim-2024.5.22.dist-info/top_level.txt,sha256=mVJT9Q6vqdBJyJ6acJvUdopsnVCQH7wEMQ-3iT6C-Jg,19
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msasim-2024.5.22.dist-info/METADATA,sha256=xZjkEbQzNYYvB1WB75UQGh14FnS4rM7CUgujkplkRkA,435
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Sailfish/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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Sailfish/simulator.py,sha256=CTFAnavIHy918aF141FKeZjO5Y-oYASI-TR5MMGGVks,24324
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{Sailfish → msasim}/__init__.py
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