msasim 24.8.1__cp310-cp310-macosx_11_0_arm64.whl → 24.8.2__cp310-cp310-macosx_11_0_arm64.whl

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Files changed (8) hide show
  1. _Sailfish.cpython-310-darwin.so +0 -0
  2. msasim/sailfish.py +8 -4
  3. {msasim-24.8.1.dist-info → msasim-24.8.2.dist-info}/METADATA +1 -1
  4. msasim-24.8.2.dist-info/RECORD +8 -0
  5. msasim-24.8.1.dist-info/RECORD +0 -8
  6. {msasim-24.8.1.dist-info → msasim-24.8.2.dist-info}/LICENSE +0 -0
  7. {msasim-24.8.1.dist-info → msasim-24.8.2.dist-info}/WHEEL +0 -0
  8. {msasim-24.8.1.dist-info → msasim-24.8.2.dist-info}/top_level.txt +0 -0
_Sailfish.cpython-310-darwin.so CHANGED
Binary file
msasim/sailfish.py CHANGED
@@ -10,6 +10,7 @@ from enum import Enum
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  MODEL_CODES = _Sailfish.modelCode
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  class SIMULATION_TYPE(Enum):
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+ NOSUBS = 0
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  DNA = 1
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  PROTEIN = 2
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@@ -413,13 +414,15 @@ class Simulator:
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  raise ValueError(f"failed to verify simProtocol")
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  if not simulation_type:
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- warnings.warn(f"simulation type not provided -> running protein simulation")
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- simulation_type = SIMULATION_TYPE.PROTEIN
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+ warnings.warn(f"simulation type not provided -> running indel only simulation")
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+ simulation_type = SIMULATION_TYPE.NOSUBS
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  if simulation_type == SIMULATION_TYPE.PROTEIN:
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  self._alphabet = _Sailfish.alphabetCode.AMINOACID
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  elif simulation_type == SIMULATION_TYPE.DNA:
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  self._alphabet = _Sailfish.alphabetCode.NUCLEOTIDE
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+ elif simulation_type == SIMULATION_TYPE.NOSUBS:
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+ self._alphabet = _Sailfish.alphabetCode.NULLCODE
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  else:
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  raise ValueError(f"unknown simulation type, please provde one of the following: {[e.name for e in SIMULATION_TYPE]}")
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@@ -525,8 +528,9 @@ class Simulator:
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  self.get_sequences_to_save())
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  # sim.init_substitution_sim(mFac)
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- substitutions = self.gen_substitutions(msa.get_length())
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- msa.fill_substitutions(substitutions)
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+ if self._simulation_type != SIMULATION_TYPE.NOSUBS:
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+ substitutions = self.gen_substitutions(msa.get_length())
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+ msa.fill_substitutions(substitutions)
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  Msas.append(msa)
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  return Msas
{msasim-24.8.1.dist-info → msasim-24.8.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: msasim
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- Version: 24.8.1
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+ Version: 24.8.2
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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-24.8.2.dist-info/RECORD ADDED
@@ -0,0 +1,8 @@
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+ _Sailfish.cpython-310-darwin.so,sha256=laP3o4tMsb3G82_o33qzHi0uKXIAqwGhWcnhKzTMvnk,1030976
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+ msasim-24.8.2.dist-info/RECORD,,
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+ msasim-24.8.2.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
4
+ msasim-24.8.2.dist-info/WHEEL,sha256=6rmwReypM7ePUybLxdjFOqbzieOVIFj4iouOv8YmcSc,109
5
+ msasim-24.8.2.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
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+ msasim-24.8.2.dist-info/METADATA,sha256=_QWIiT1s3BrrlEHtkV6meCXo8ECvIRBbp2hFaRnKbYQ,1467
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+ msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ msasim/sailfish.py,sha256=T8WrLsERNh4vQlqS3nM5dAo-MLdpVOVjNcOm49KKwaI,24764
msasim-24.8.1.dist-info/RECORD DELETED
@@ -1,8 +0,0 @@
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- _Sailfish.cpython-310-darwin.so,sha256=bEZjBDGGJfn1NqALn7UGYk9SJj6_iZ-hmUu35l9IAuA,1011664
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- msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- msasim/sailfish.py,sha256=CYb-zMuUKtNt-sDeK9sawSD_7S2bf0ctqNnBPsZQbKs,24558
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- msasim-24.8.1.dist-info/RECORD,,
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- msasim-24.8.1.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
6
- msasim-24.8.1.dist-info/WHEEL,sha256=6rmwReypM7ePUybLxdjFOqbzieOVIFj4iouOv8YmcSc,109
7
- msasim-24.8.1.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
8
- msasim-24.8.1.dist-info/METADATA,sha256=2ck3mfQWO0aL1zeFn0QN7H7QTajj5283MF-FoJI33QE,1467