pyLoopSage 1.0.7__tar.gz → 1.0.9__tar.gz

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.7
+Version: 1.0.9
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.7"
+__version__ = "1.0.9"

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/loopsage/args_definition.py

@@ -123,8 +123,8 @@ available_platforms = [mm.Platform.getPlatform(i).getName() for i in range(mm.Pl
 
 args = ListOfArgs([
     # Platform settings
-    Arg('PLATFORM', help=f"name of the platform. Available choices: {' '.join(available_platforms)}", type=str, default='CPU', val='CPU'),
-    Arg('DEVICE', help="device index for CUDA or OpenCL (count from 0)", type=str, default='', val=''),
+    Arg('PLATFORM', help=f"Name of the platform. Available choices: {' '.join(available_platforms)}", type=str, default='CPU', val='CPU'),
+    Arg('DEVICE', help="Device index for CUDA or OpenCL (count from 0)", type=str, default='', val=''),
     
     # Input data
     Arg('N_BEADS', help="Number of Simulation Beads.", type=int, default='', val=''),
@@ -138,7 +138,7 @@ args = ListOfArgs([
     Arg('LEF_RW', help="True in case that you would like to make cohesins slide as random walk, instead of sliding only in one direction.", type=bool, default='True', val='True'),
     Arg('N_STEPS', help="Number of Monte Carlo steps.", type=int, default='', val=''),
     Arg('N_LEF', help="Number of loop extrusion factors (condensins and cohesins).", type=int, default='', val=''),
-    Arg('MC_STEP', help="Monte Carlo frequency.", type=int, default='200', val='200'),
+    Arg('MC_STEP', help="Monte Carlo frequency. It should be hundreds of steps, except if you would like to include molecular dynamics (MD) and in this case it should be ideally 1.", type=int, default='200', val='200'),
     Arg('BURNIN', help="Burnin-period (steps that are considered before equillibrium).", type=int, default='1000', val='1000'),
     Arg('T_INIT', help="Initial Temperature of the Stochastic Model.", type=float, default='1.8', val='1.8'),
     Arg('T_FINAL', help="Final Temperature of the Stochastic Model.", type=float, default='0.01', val='0.01'),
@@ -146,6 +146,8 @@ args = ListOfArgs([
     Arg('FOLDING_COEFF', help="Folding coefficient.", type=float, default='1.0', val='1.0'),
     Arg('CROSS_COEFF', help="LEF crossing coefficient.", type=float, default='1.0', val='1.0'),
     Arg('BIND_COEFF', help="CTCF binding coefficient.", type=float, default='1.0', val='1.0'),
+    Arg('SAVE_PLOTS', help="It should be true in case that you would like to save diagnostic plots. In case that you use small MC_STEP or large N_STEPS is better to mark it as False.", type=bool, default='True', val='True'),
+    Arg('SAVE_MDT', help="In case that you would liketo save metadata of the stochastic simulation.", type=bool, default='True', val='True'),
 
     # Molecular Dynamic Properties
     Arg('INITIAL_STRUCTURE_TYPE', help="you can choose between: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.", type=str, default='rw', val='rw'),
@@ -158,6 +160,7 @@ args = ListOfArgs([
     Arg('EV_FF_STRENGTH', help="Excluded-volume strength.", type=float, default='10.0', val='10.0'),
     Arg('FRICTION',help='Friction coefficient of the Langevin integrator.',type=float, default='0.1', val='0.1'),
     Arg('TOLERANCE', help="Tolerance that works as stopping condition for energy minimization.", type=float, default='0.001', val='0.001'),
-    Arg('SIM_TEMP', help="The temperature of the stochastic simulation.", type=Quantity, default='310 kelvin', val='310 kelvin'),
-    Arg('SIM_STEP', help="This is the amount of simulation steps that are perform each time that we change the loop forces. If this number is too high, the simulation is slow, if is too low it may not have enough time to adapt the structure to the new constraints.", type=int, default='100', val='100'),
-])
+    Arg('VIZ_HEATS', help="Visualize the output average heatmap.", type=bool, default='True', val='True'),
+    Arg('SIM_TEMP', help="The temperature of the 3D simulation (EM or MD).", type=Quantity, default='310 kelvin', val='310 kelvin'),
+    Arg('SIM_STEP', help="This is the amount of simulation steps that are perform each time that we change the loop forces. If this number is too high, the simulation is slow, if is too low it may not have enough time to adapt the structure to the new constraints.", type=int, default='10', val='10'),
+])

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/loopsage/em.py

@@ -68,17 +68,18 @@ class EM_LE:
         print('Energy minimizations done :D\n')
 
         self.avg_heat = sum_heat/counter
-        np.save(self.path+f'/other/avg_heatmap.npy',self.avg_heat)
+        
         if plots:
             figure(figsize=(10, 10))
             plt.imshow(self.avg_heat,cmap="Reds",vmax=1)
             plt.colorbar()
+            np.save(self.path+f'/other/avg_heatmap.npy',self.avg_heat)
             plt.savefig(self.path+f'/plots/avg_heatmap.svg',format='svg',dpi=500)
             plt.savefig(self.path+f'/plots/avg_heatmap.pdf',format='pdf',dpi=500)
             # plt.colorbar()
             plt.close()
             
-            return self.avg_heat
+        return self.avg_heat
 
     def add_forcefield(self,ms,ns):
         '''
@@ -96,7 +97,7 @@ class EM_LE:
         self.ev_force.addPerParticleParameter('sigma')
         self.system.addForce(self.ev_force)
         for i in range(self.system.getNumParticles()):
-            self.ev_force.addParticle([0.1])
+            self.ev_force.addParticle([0.05])
 
         # Harmonic bond borce between succesive beads
         self.bond_force = mm.HarmonicBondForce()

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/loopsage/md.py

@@ -94,12 +94,13 @@ class MD_LE:
 
             self.avg_heat = np.average(heats,axis=0)
             self.std_heat = np.std(heats,axis=0)
-            np.save(self.path+f'/other/avg_heatmap.npy',self.avg_heat)
-            np.save(self.path+f'/other/std_heatmap.npy',self.std_heat)
+            
             if plots:
+                np.save(self.path+f'/other/avg_heatmap.npy',self.avg_heat)
+                np.save(self.path+f'/other/std_heatmap.npy',self.std_heat)
                 self.plot_heat(self.avg_heat,f'/plots/avg_heatmap.svg')
                 self.plot_heat(self.std_heat,f'/plots/std_heatmap.svg')
-            return self.avg_heat
+        return self.avg_heat
     
     def change_loop(self,i):
         force_idx = self.system.getNumForces()-1

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/loopsage/run.py

@@ -70,11 +70,11 @@ def main():
     
     # Run Simulation
     sim = StochasticSimulation(region,chrom,bedpe_file,out_dir=output_name,N_beads=N_beads,N_lef=N_lef)
-    Es, Ms, Ns, Bs, Ks, Fs, ufs = sim.run_energy_minimization(N_steps,MC_step,burnin,T,T_min,mode=mode,viz=True,save=True,lef_rw=args.LEF_RW)
+    Es, Ms, Ns, Bs, Ks, Fs, ufs = sim.run_energy_minimization(N_steps,MC_step,burnin,T,T_min,mode=mode,viz=args.SAVE_PLOTS,save=args.SAVE_MDT,lef_rw=args.LEF_RW)
     if args.SIMULATION_TYPE=='EM':
-        sim.run_EM(args.PLATFORM,args.ANGLE_FF_STRENGTH,args.LE_FF_LENGTH,args.LE_FF_STRENGTH,args.EV_FF_STRENGTH,args.TOLERANCE,args.FRICTION,args.INTEGRATOR_STEP,args.SIM_TEMP)
+        sim.run_EM(args.PLATFORM,args.ANGLE_FF_STRENGTH,args.LE_FF_LENGTH,args.LE_FF_STRENGTH,args.EV_FF_STRENGTH,args.TOLERANCE,args.FRICTION,args.INTEGRATOR_STEP,args.SIM_TEMP,args.VIZ_HEATS)
     elif args.SIMULATION_TYPE=='MD':
-        sim.run_MD(args.PLATFORM,args.ANGLE_FF_STRENGTH,args.LE_FF_LENGTH,args.LE_FF_STRENGTH,args.EV_FF_STRENGTH,args.TOLERANCE,args.FRICTION,args.INTEGRATOR_STEP,args.SIM_TEMP,args.SIM_STEP)
+        sim.run_MD(args.PLATFORM,args.ANGLE_FF_STRENGTH,args.LE_FF_LENGTH,args.LE_FF_STRENGTH,args.EV_FF_STRENGTH,args.TOLERANCE,args.FRICTION,args.INTEGRATOR_STEP,args.SIM_TEMP,args.SIM_STEP,args.VIZ_HEATS)
     elif args.SIMULATION_TYPE==None:
         print('\n3D simulation did not run because it was not specified. Please specify argument SIMULATION_TYPE as EM or MD.')
     else:

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/loopsage/stochastic_simulation.py

@@ -272,14 +272,14 @@ class StochasticSimulation:
         self.N_CTCF = np.max([np.count_nonzero(self.L),np.count_nonzero(self.R)])
         print('Number of CTCF:',self.N_CTCF)
 
-    def run_EM(self,platform='CPU',angle_ff_strength=200,le_distance=0.0,le_ff_strength=300000.0,ev_ff_strength=10.0,tolerance=0.001,friction=0.1,integrator_step=5*mm.unit.femtosecond,temperature=310):
+    def run_EM(self,platform='CPU',angle_ff_strength=200,le_distance=0.0,le_ff_strength=300000.0,ev_ff_strength=10.0,tolerance=0.001,friction=0.1,integrator_step=5*mm.unit.femtosecond,temperature=310,save_plots=True):
         em = EM_LE(self.Ms,self.Ns,self.N_beads,self.burnin,self.MC_step,self.path,platform,angle_ff_strength,le_distance,le_ff_strength,ev_ff_strength,tolerance)
-        sim_heat = em.run_pipeline(plots=True,friction=friction,integrator_step=integrator_step,temperature=temperature)
+        sim_heat = em.run_pipeline(plots=save_plots,friction=friction,integrator_step=integrator_step,temperature=temperature)
         corr_exp_heat(sim_heat,self.bedpe_file,self.region,self.chrom,self.N_beads,self.path)
-
-    def run_MD(self,platform='CPU',angle_ff_strength=200,le_distance=0.0,le_ff_strength=300000.0,ev_ff_strength=10.0,tolerance=0.001,friction=0.1,integrator_step=5*mm.unit.femtosecond,temperature=310,sim_step=100):
+    
+    def run_MD(self,platform='CPU',angle_ff_strength=200,le_distance=0.0,le_ff_strength=300000.0,ev_ff_strength=10.0,tolerance=0.001,friction=0.1,integrator_step=5*mm.unit.femtosecond,temperature=310,sim_step=100,save_plots=True):
         md = MD_LE(self.Ms,self.Ns,self.N_beads,self.burnin,self.MC_step,self.path,platform,angle_ff_strength,le_distance,le_ff_strength,ev_ff_strength,tolerance)
-        sim_heat = md.run_pipeline(plots=True,sim_step=sim_step,friction=friction,integrator_step=integrator_step,temperature=temperature)
+        sim_heat = md.run_pipeline(plots=save_plots,sim_step=sim_step,friction=friction,integrator_step=integrator_step,temperature=temperature)
         corr_exp_heat(sim_heat,self.bedpe_file,self.region,self.chrom,self.N_beads,self.path)
 
 def main():

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/pyLoopSage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.7
+Version: 1.0.9
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.7 → pyloopsage-1.0.9}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='1.0.7',  # Version of the software
+    version='1.0.9',  # Version of the software
     description='An energy-based stochastic model of loop extrusion in chromatin.',
     long_description=long_description,
     long_description_content_type='text/markdown',