msasim 24.10.4__cp312-cp312-musllinux_1_2_x86_64.whl → 24.13.0__cp312-cp312-musllinux_1_2_x86_64.whl

msasim/sailfish.py

@@ -1,5 +1,5 @@
 import _Sailfish
-import os, warnings, math, operator, time, profile
+import os, warnings, math, operator, time, profile, tempfile, pathlib
 from functools import reduce
 from typing import List, Optional, Dict
 from re import split
@@ -101,12 +101,9 @@ class ZipfDistribution(Distribution):
         """
         self.p = p
         self.truncation = truncation
-        HARMONIC = lambda n,s: sum([(i**-s) for i in range(1,n+1)])
-        PMF = lambda x: (x**-p)*(1.0/HARMONIC(truncation, p))
-        CDF = lambda x: HARMONIC(x, p) / HARMONIC(truncation, p)
-        norm_factor = CDF(truncation) - CDF(0)
 
-        probabilities = [PMF(i)/norm_factor for i in range(1, truncation+1)]
+        norm_factor = sum([(i**-p) for i in range(1,truncation+1)])
+        probabilities = [(i**-p)/norm_factor for i in range(1, truncation+1)]
 
         self.set_dist(probabilities)
     
@@ -465,15 +462,16 @@ class Simulator:
     def set_replacement_model(
             self,
             model: _Sailfish.modelCode,
+            amino_model_file: pathlib.Path = None,
             model_parameters: List = None,
             gamma_parameters_alpha : float = 1.0,
-            gamma_parameters_catergories: int = 1,
+            gamma_parameters_categories: int = 1,
             invariant_sites_proportion: float = 0.0
         ) -> None:
         if not model:
             raise ValueError(f"please provide a substitution model from the the following list: {_Sailfish.modelCode}")
-        if int(gamma_parameters_catergories) != gamma_parameters_catergories:
-            raise ValueError(f"gamma_parameters_catergories has to be a positive int value: received value of {gamma_parameters_catergories}")
+        if int(gamma_parameters_categories) != gamma_parameters_categories:
+            raise ValueError(f"gamma_parameters_catergories has to be a positive int value: received value of {gamma_parameters_categories}")
         self._model_factory = _Sailfish.modelFactory(self._simProtocol._get_Sailfish_tree())
 
         self._model_factory.set_alphabet(self._alphabet)
@@ -481,6 +479,8 @@ class Simulator:
             if model_parameters:
                 raise ValueError(f"no model parameters are used in protein, recevied value of: {model_parameters}")
             self._model_factory.set_replacement_model(model)
+            if model == MODEL_CODES.CUSTOM and amino_model_file:
+                self._model_factory.set_amino_replacement_model_file(str(amino_model_file))
         else:
             if model == MODEL_CODES.NUCJC and model_parameters:
                 raise ValueError(f"no model parameters in JC model, recevied value of: {model_parameters}")
@@ -492,7 +492,7 @@ class Simulator:
             else:
                 self._model_factory.set_model_parameters(model_parameters)
 
-        self._model_factory.set_gamma_parameters(gamma_parameters_alpha, gamma_parameters_catergories)
+        self._model_factory.set_gamma_parameters(gamma_parameters_alpha, gamma_parameters_categories)
         self._model_factory.set_invariant_sites_proportion(invariant_sites_proportion)
         self._simulator.init_substitution_sim(self._model_factory)
 
@@ -537,6 +537,26 @@ class Simulator:
             Msas.append(msa)
         return Msas
     
+    def simulate_low_memory(self, output_file_path: pathlib.Path) -> Msa:
+        if self._simProtocol._is_insertion_rate_zero and self._simProtocol._is_deletion_rate_zero:
+            msa = Msa(sum(self.get_sequences_to_save()),
+                        self._simProtocol.get_sequence_size(),
+                        self.get_sequences_to_save())
+        else:
+            blocktree = self.gen_indels()
+            msa = Msa(blocktree._get_Sailfish_blocks(),
+                        self._simProtocol._get_root(),
+                        self.get_sequences_to_save())
+
+        # sim.init_substitution_sim(mFac)
+        if self._simulation_type != SIMULATION_TYPE.NOSUBS:
+            with tempfile.TemporaryDirectory() as tmpdirname:
+                self._simulator.gen_substitutions_to_dir(msa.get_length(), tmpdirname)
+                msa._msa.set_substitutions_folder(tmpdirname)
+                msa._msa.write_msa_from_dir(str(output_file_path))
+
+
+    
     def __call__(self) -> Msa:
         return self.simulate(1)[0]
     

{msasim-24.10.4.dist-info → msasim-24.13.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.10.4
+Version: 24.13.0
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda
@@ -9,7 +9,7 @@ Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Provides-Extra: test
-Requires-Dist: pytest ; extra == 'test'
+Requires-Dist: pytest; extra == "test"
 
 # Sailfish
 

msasim-24.13.0.dist-info/RECORD

@@ -0,0 +1,10 @@
+_Sailfish.cpython-312-x86_64-linux-musl.so,sha256=ABg26WKU9PLRpgPJ4BshHDT3poGdm0kEAmXCBjIUH1U,1344945
+msasim.libs/libstdc++-496613c0.so.6.0.32,sha256=AwZhL5WFT99I2Q6vIxXOhW7qddfuOZ1xecxiP9QTVY4,3494361
+msasim.libs/libgcc_s-a3a07607.so.1,sha256=5ptIUeAzZweNZrFehN0_Bb5B0FcJgux7NbAFoU8vwwo,148041
+msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msasim/sailfish.py,sha256=o_6N1f1rFXgG0z_b17CJRC3wUzIcoKy__c6s1FroHgI,25901
+msasim-24.13.0.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
+msasim-24.13.0.dist-info/RECORD,,
+msasim-24.13.0.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
+msasim-24.13.0.dist-info/METADATA,sha256=EnhB_caqxOZOhmTtV7wOJSzEMx-HZyXE4OjlwKsVdVQ,1467
+msasim-24.13.0.dist-info/WHEEL,sha256=0YqoKpIYqm37NqpTXnSSuBR8luVWM2UMssZySUeF554,112

{msasim-24.10.4.dist-info → msasim-24.13.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: false
 Tag: cp312-cp312-musllinux_1_2_x86_64
 

msasim-24.10.4.dist-info/RECORD

@@ -1,10 +0,0 @@
-_Sailfish.cpython-312-x86_64-linux-musl.so,sha256=39mZDrQz8u928itDmqF9QSYhwizzHxCmX2RdqsmSmNc,1315321
-msasim.libs/libstdc++-496613c0.so.6.0.32,sha256=AwZhL5WFT99I2Q6vIxXOhW7qddfuOZ1xecxiP9QTVY4,3494361
-msasim.libs/libgcc_s-a3a07607.so.1,sha256=5ptIUeAzZweNZrFehN0_Bb5B0FcJgux7NbAFoU8vwwo,148041
-msasim-24.10.4.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
-msasim-24.10.4.dist-info/METADATA,sha256=lcUfw5rRfQ2FfAc8yEwU8I82UHWQp-r_WFW_PnsGP0U,1468
-msasim-24.10.4.dist-info/RECORD,,
-msasim-24.10.4.dist-info/WHEEL,sha256=BwYrisTu1yp8WloXcEi-3Rmdx-uar3nqcuXFSFGpP_Q,112
-msasim-24.10.4.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
-msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-msasim/sailfish.py,sha256=xcSh3Q4fo-PiQVjYQgqcqCV3sJ-u32jdMhsJJAL9vHY,24896