msasim 25.10.21__cp311-cp311-win_amd64.whl → 25.11.2__cp311-cp311-win_amd64.whl

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Files changed (8) hide show
  1. _Sailfish.cp311-win_amd64.pyd +0 -0
  2. msasim/sailfish.py +6 -5
  3. {msasim-25.10.21.dist-info → msasim-25.11.2.dist-info}/METADATA +1 -1
  4. msasim-25.11.2.dist-info/RECORD +10 -0
  5. msasim-25.10.21.dist-info/RECORD +0 -10
  6. {msasim-25.10.21.dist-info → msasim-25.11.2.dist-info}/WHEEL +0 -0
  7. {msasim-25.10.21.dist-info → msasim-25.11.2.dist-info}/licenses/LICENSE +0 -0
  8. {msasim-25.10.21.dist-info → msasim-25.11.2.dist-info}/top_level.txt +0 -0
_Sailfish.cp311-win_amd64.pyd CHANGED
Binary file
msasim/sailfish.py CHANGED
@@ -415,7 +415,10 @@ class Simulator:
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  # verify sim_protocol
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  if self._verify_sim_protocol(simProtocol):
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  self._simProtocol = simProtocol
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- self._simulator = _Sailfish.Simulator(self._simProtocol._sim)
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+ if simulation_type == SIMULATION_TYPE.PROTEIN:
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+ self._simulator = _Sailfish.AminoSimulator(self._simProtocol._sim)
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+ else:
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+ self._simulator = _Sailfish.NucleotideSimulator(self._simProtocol._sim)
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  else:
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  raise ValueError(f"failed to verify simProtocol")
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@@ -559,13 +562,11 @@ class Simulator:
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  msa = Msa(blocktree._get_Sailfish_blocks(),
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  self._simProtocol._get_root(),
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  self.get_sequences_to_save())
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+ self._simulator.set_aligned_sequence_map(msa._msa)
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  # sim.init_substitution_sim(mFac)
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  if self._simulation_type != SIMULATION_TYPE.NOSUBS:
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- with tempfile.TemporaryDirectory() as tmpdirname:
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- self._simulator.gen_substitutions_to_dir(msa.get_length(), tmpdirname)
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- msa._msa.set_substitutions_folder(tmpdirname)
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- msa._msa.write_msa_from_dir(str(output_file_path))
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+ self._simulator.gen_substitutions_to_file(msa.get_length(), str(output_file_path))
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{msasim-25.10.21.dist-info → msasim-25.11.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: msasim
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- Version: 25.10.21
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+ Version: 25.11.2
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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
msasim-25.11.2.dist-info/RECORD ADDED
@@ -0,0 +1,10 @@
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+ _Sailfish.cp311-win_amd64.pyd,sha256=W0DdYWa0ahooaNZ-NAOxEqQvRli2wrpHMWWPv4aJXG0,607232
2
+ _Sailfish/__init__.pyi,sha256=kic4k1SjpXin4g8Ztzk8cDkMZpE8Hi-yIfkjp5g6RRI,15688
3
+ _Sailfish/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
4
+ msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
5
+ msasim/sailfish.py,sha256=KA-DpYKS8KpgLKrjUEOD6jPizw_P0F9LknfuzMJ8ZEM,27021
6
+ msasim-25.11.2.dist-info/licenses/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
7
+ msasim-25.11.2.dist-info/METADATA,sha256=jdn8JdjM7CPMLwm6-Ba2QIkYz-NDSWlOSMtUW75Qg-E,1730
8
+ msasim-25.11.2.dist-info/WHEEL,sha256=JLOMsP7F5qtkAkINx5UnzbFguf8CqZeraV8o04b0I8I,101
9
+ msasim-25.11.2.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
10
+ msasim-25.11.2.dist-info/RECORD,,
msasim-25.10.21.dist-info/RECORD DELETED
@@ -1,10 +0,0 @@
1
- _Sailfish.cp311-win_amd64.pyd,sha256=Sjf1586a6vlujFQdXmzSZxRGvsE_N3kUCP5MhXYrSzU,625152
2
- _Sailfish/__init__.pyi,sha256=kic4k1SjpXin4g8Ztzk8cDkMZpE8Hi-yIfkjp5g6RRI,15688
3
- _Sailfish/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
4
- msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
5
- msasim/sailfish.py,sha256=73JwceDHShxQOQ3c5QxsLsvWvOf_A5FWeCKOKRpqIaQ,26966
6
- msasim-25.10.21.dist-info/licenses/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
7
- msasim-25.10.21.dist-info/METADATA,sha256=SvxG2VwLQ0C_jUi1BdVoU3Zkk4Ktwultzz7Va7h8PWc,1731
8
- msasim-25.10.21.dist-info/WHEEL,sha256=JLOMsP7F5qtkAkINx5UnzbFguf8CqZeraV8o04b0I8I,101
9
- msasim-25.10.21.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
10
- msasim-25.10.21.dist-info/RECORD,,