msasim 2024.5.22__cp36-cp36m-musllinux_1_1_x86_64.whl → 2024.5.221253__cp36-cp36m-musllinux_1_1_x86_64.whl

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Files changed (9) hide show
  1. msasim-2024.5.221253.dist-info/METADATA +57 -0
  2. msasim-2024.5.221253.dist-info/RECORD +10 -0
  3. {msasim-2024.5.22.dist-info → msasim-2024.5.221253.dist-info}/top_level.txt +1 -1
  4. msasim-2024.5.22.dist-info/METADATA +0 -16
  5. msasim-2024.5.22.dist-info/RECORD +0 -10
  6. {Sailfish → msasim}/__init__.py +0 -0
  7. /Sailfish/simulator.py → /msasim/sailfish.py +0 -0
  8. {msasim-2024.5.22.dist-info → msasim-2024.5.221253.dist-info}/LICENSE +0 -0
  9. {msasim-2024.5.22.dist-info → msasim-2024.5.221253.dist-info}/WHEEL +0 -0
msasim-2024.5.221253.dist-info/METADATA ADDED
@@ -0,0 +1,57 @@
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+ Metadata-Version: 2.1
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+ Name: msasim
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+ Version: 2024.5.221253
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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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+ License: UNKNOWN
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+ Platform: UNKNOWN
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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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+
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+ # Sailfish
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+
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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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+
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+ ## Project goals
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+
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+ - Ease of use
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+ - Speed
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+ - Modularity
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install msasim
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+ ```
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+
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+ ## Example
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+
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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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+
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+ ROOT_SEQUENCE_LENGTH = 100
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+
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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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+
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+ simulation = sim.Simulator(sim_protocol, simulation_type=sim.SIMULATION_TYPE.PROTEIN)
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+
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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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+ ```
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+
msasim-2024.5.221253.dist-info/RECORD ADDED
@@ -0,0 +1,10 @@
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+ _Sailfish.cpython-36m-x86_64-linux-gnu.so,sha256=wDu66tG2DnoqDsSenpvNOX-4aZfg17hyBs9-NRyKfOo,1199161
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+ msasim-2024.5.221253.dist-info/WHEEL,sha256=rbVfYZzJiOCEiiKDVkaog3MWj3SC9SfTJ-H92vzqnHY,112
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+ msasim-2024.5.221253.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
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+ msasim-2024.5.221253.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
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+ msasim-2024.5.221253.dist-info/RECORD,,
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+ msasim-2024.5.221253.dist-info/METADATA,sha256=NXMh1B3AXOl9h1fFJ5MLF3cSQ42v8i_8m9JVGwm_14o,1510
7
+ msasim.libs/libstdc++-a9383cce.so.6.0.28,sha256=Wy9UCdwS1rwI9GU5e7qE61S0AkRqqwti1q_adWSs-Rk,2447393
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+ msasim.libs/libgcc_s-a04fdf82.so.1,sha256=YxqJNaesQMhDswHEQpXsiLnVvMBBbYO6KYMDZFPWKSM,81257
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+ msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ msasim/sailfish.py,sha256=CTFAnavIHy918aF141FKeZjO5Y-oYASI-TR5MMGGVks,24324
{msasim-2024.5.22.dist-info → msasim-2024.5.221253.dist-info}/top_level.txt RENAMED
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- Sailfish
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  _Sailfish
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+ msasim
msasim-2024.5.22.dist-info/METADATA DELETED
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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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- License: UNKNOWN
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- Platform: UNKNOWN
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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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-
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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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-
msasim-2024.5.22.dist-info/RECORD DELETED
@@ -1,10 +0,0 @@
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- _Sailfish.cpython-36m-x86_64-linux-gnu.so,sha256=wDu66tG2DnoqDsSenpvNOX-4aZfg17hyBs9-NRyKfOo,1199161
2
- Sailfish/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- Sailfish/simulator.py,sha256=CTFAnavIHy918aF141FKeZjO5Y-oYASI-TR5MMGGVks,24324
4
- msasim.libs/libstdc++-a9383cce.so.6.0.28,sha256=Wy9UCdwS1rwI9GU5e7qE61S0AkRqqwti1q_adWSs-Rk,2447393
5
- msasim.libs/libgcc_s-a04fdf82.so.1,sha256=YxqJNaesQMhDswHEQpXsiLnVvMBBbYO6KYMDZFPWKSM,81257
6
- msasim-2024.5.22.dist-info/WHEEL,sha256=rbVfYZzJiOCEiiKDVkaog3MWj3SC9SfTJ-H92vzqnHY,112
7
- msasim-2024.5.22.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
8
- msasim-2024.5.22.dist-info/top_level.txt,sha256=mVJT9Q6vqdBJyJ6acJvUdopsnVCQH7wEMQ-3iT6C-Jg,19
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- msasim-2024.5.22.dist-info/RECORD,,
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- msasim-2024.5.22.dist-info/METADATA,sha256=2gIzialKFhrP-FmN1o7Lf_kGyAWPBHxu6WwX44JkQI0,471
{Sailfish → msasim}/__init__.py RENAMED
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/Sailfish/simulator.py → /msasim/sailfish.py RENAMED
File without changes