msasim 24.10.4__cp38-cp38-win_amd64.whl → 24.12.0__cp38-cp38-win_amd64.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.cp38-win_amd64.pyd,sha256=zY0asthjGJK060sL8T0lttcx4DTpCb0aR3F0dftl0Gs,608768
+msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msasim/sailfish.py,sha256=ElArIFObfW_1qc8no5Q0DKqTDwuF15lFibEVV0wUqzM,26261
+msasim-24.12.0.dist-info/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
+msasim-24.12.0.dist-info/METADATA,sha256=95EV7J2PoOQ0yavAR20_fSxzndd82B_mzi04tAfOtrA,1522
+msasim-24.12.0.dist-info/WHEEL,sha256=rTcqimtzpX3smAWAhGmiRSWAxTY4PqYPNE-p4kscHDQ,99
+msasim-24.12.0.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
+msasim-24.12.0.dist-info/RECORD,,

{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-win_amd64
 

msasim-24.10.4.dist-info/RECORD

@@ -1,8 +0,0 @@
-_Sailfish.cp38-win_amd64.pyd,sha256=16hamv0pyoarn0vhdHTc0mvl-qdQ9JH1yveSp6BuZZc,578560
-msasim/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-msasim/sailfish.py,sha256=A9ETx3KB9sFHaYP4dcR5aaPjts9VbUhSmOR04qTzn-Q,25442
-msasim-24.10.4.dist-info/LICENSE,sha256=MgvumWWAhx44Y7XYvLMzqDUZv_Mn4nZLuC-EBl9E0l0,10483
-msasim-24.10.4.dist-info/METADATA,sha256=6yT55WNrZ-6ie4KblmXszp1BuK4N19yI-0j667hb8wc,1522
-msasim-24.10.4.dist-info/WHEEL,sha256=1rwUt2BQv3N5S0pE0N9WlEu1uiKd-mQhEp4H-4r377U,99
-msasim-24.10.4.dist-info/top_level.txt,sha256=NS1ILx5V94Yyh_M7yDrrqbBPu1TL_zJuxhsI90YEJVY,17
-msasim-24.10.4.dist-info/RECORD,,