msasim 24.10.4__cp38-cp38-macosx_11_0_arm64.whl → 24.12.0__cp38-cp38-macosx_11_0_arm64.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)
     
@@ -537,6 +534,26 @@ 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-24.12.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: msasim
-Version: 24.10.4
+Version: 24.12.0
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

msasim-24.12.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+_Sailfish.cpython-38-darwin.so,sha256=OHUmypNnIk1kN2jFIwkUl96MUzlKmmkNaiupSbgonsg,1076560
+msasim-24.12.0.dist-info/RECORD,,
+msasim-24.12.0.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
+msasim-24.12.0.dist-info/WHEEL,sha256=7_oe0rMIEoZOpgBhth1WRv0SCKz8pdiUZgyT0NjKRv8,107
+msasim-24.12.0.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
+msasim-24.12.0.dist-info/METADATA,sha256=jVxAKL5akbzugkbsmgzPnFcQ2_kc84Pu18k0V4d1_bE,1468
+msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msasim/sailfish.py,sha256=I45ufK0owZIsu7zOBN427rQ07RGl3Jll8mnGiCS0Ufo,25698

{msasim-24.10.4.dist-info → msasim-24.12.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.3.0)
 Root-Is-Purelib: false
 Tag: cp38-cp38-macosx_11_0_arm64
 

msasim-24.10.4.dist-info/RECORD

@@ -1,8 +0,0 @@
-_Sailfish.cpython-38-darwin.so,sha256=caVXqMAMaOwI6Dw1Xk6uOgP99ow40cFP56Mt4BdWaFw,1054112
-msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-msasim/sailfish.py,sha256=xcSh3Q4fo-PiQVjYQgqcqCV3sJ-u32jdMhsJJAL9vHY,24896
-msasim-24.10.4.dist-info/RECORD,,
-msasim-24.10.4.dist-info/LICENSE,sha256=p1Aa_mM2Nu6dG3XqMVU62Jhf04lNOwtXUrhhvhcDips,10312
-msasim-24.10.4.dist-info/WHEEL,sha256=EiRgcuXdFyaNkKNNUWj3dZKym6WxDBm6glUi0Kcah-U,107
-msasim-24.10.4.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
-msasim-24.10.4.dist-info/METADATA,sha256=lcUfw5rRfQ2FfAc8yEwU8I82UHWQp-r_WFW_PnsGP0U,1468