pyLoopSage 1.0.9__tar.gz → 1.0.11__tar.gz

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.9
+Version: 1.0.11
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.9"
+__version__ = "1.0.10"

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/loopsage/args_definition.py

@@ -136,12 +136,12 @@ args = ListOfArgs([
     
     # Stochastic Simulation parameters
     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_STEPS', help="Number of Monte Carlo steps.", type=int, default='40000', val='40000'),
     Arg('N_LEF', help="Number of loop extrusion factors (condensins and cohesins).", type=int, default='', val=''),
-    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('MC_STEP', help="Monte Carlo frequency. It should be hundreds of steps so as to avoid autocorrelated ensembles.", 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'),
+    Arg('T_INIT', help="Initial Temperature of the Stochastic Model.", type=float, default='2.0', val='2.0'),
+    Arg('T_FINAL', help="Final Temperature of the Stochastic Model.", type=float, default='1.0', val='1.0'),
     Arg('METHOD', help="Stochastic modelling method. It can be Metropolis or Simulated Annealing.", type=str, default='Annealing', val='Annealing'),
     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'),
@@ -152,15 +152,15 @@ args = ListOfArgs([
     # 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'),
     Arg('SIMULATION_TYPE', help="It can be either EM (multiple energy minimizations) or MD (one energy minimization and then run molecular dynamics).", type=str, default='', val=''),
-    Arg('INTEGRATOR_STEP', help="The step of the integrator.", type=Quantity, default='5 femtosecond', val='5 femtosecond'),
+    Arg('INTEGRATOR_STEP', help="The step of the integrator.", type=Quantity, default='100 femtosecond', val='100 femtosecond'),
     Arg('FORCEFIELD_PATH', help="Path to XML file with forcefield.", type=str, default='forcefield/classic_sm_ff.xml', val='forcefield/classic_sm_ff.xml'),
     Arg('ANGLE_FF_STRENGTH', help="Angle force strength.", type=float, default='200.0', val='200.0'),
     Arg('LE_FF_LENGTH', help="Equillibrium distance of loop forces.", type=float, default='0.1', val='0.1'),
-    Arg('LE_FF_STRENGTH', help="Interaction Strength of loop forces.", type=float, default='3000.0', val='3000.0'),
+    Arg('LE_FF_STRENGTH', help="Interaction Strength of loop forces.", type=float, default='50000.0', val='50000.0'),
     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('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'),
+    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='1000', val='1000'),
 ])

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/loopsage/em.py

@@ -12,7 +12,7 @@ from .utils import *
 from .initial_structures import *
 
 class EM_LE:
-    def __init__(self,M,N,N_beads,burnin,MC_step,path=None,platform='CPU',angle_ff_strength=200,le_distance=0.1,le_ff_strength=300000.0,ev_ff_strength=10.0,tolerance=0.001):
+    def __init__(self,M,N,N_beads,burnin,MC_step,path=None,platform='CPU',angle_ff_strength=200,le_distance=0.1,le_ff_strength=50000.0,ev_ff_strength=10.0,tolerance=0.001):
         '''
         M, N (np arrays): Position matrix of two legs of cohesin m,n. 
                           Rows represent  loops/cohesins and columns represent time
@@ -31,7 +31,7 @@ class EM_LE:
         self.ev_ff_strength = ev_ff_strength
         self.tolerance = tolerance
     
-    def run_pipeline(self,plots=False, friction=0.1, integrator_step = 5 * mm.unit.femtosecond, temperature = 310):
+    def run_pipeline(self,plots=False, friction=0.1, ff_path='forcefields/classic_sm_ff.xml', integrator_step = 100 * mm.unit.femtosecond, temperature = 310):
         '''
         This is the basic function that runs the molecular simulation pipeline.
         '''
@@ -48,7 +48,7 @@ class EM_LE:
         for i in tqdm(range(self.burnin,self.N_steps)):
             # Define System
             pdb = PDBxFile(self.path+'/LE_init_struct.cif')
-            forcefield = ForceField('forcefields/classic_sm_ff.xml')
+            forcefield = ForceField(ff_path)
             self.system = forcefield.createSystem(pdb.topology, nonbondedCutoff=1*u.nanometer)
             integrator = mm.LangevinIntegrator(temperature, friction, integrator_step)
 

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/loopsage/md.py

@@ -16,7 +16,7 @@ from .utils import *
 from .initial_structures import *
 
 class MD_LE:
-    def __init__(self,M,N,N_beads,burnin,MC_step,path=None,platform='CPU',angle_ff_strength=200,le_distance=0.1,le_ff_strength=30000.0,ev_ff_strength=10.0,tolerance=0.001):
+    def __init__(self,M,N,N_beads,burnin,MC_step,path=None,platform='CPU',angle_ff_strength=200,le_distance=0.1,le_ff_strength=50000.0,ev_ff_strength=10.0,tolerance=0.001):
         '''
         M, N (np arrays): Position matrix of two legs of cohesin m,n. 
                           Rows represent  loops/cohesins and columns represent time
@@ -35,7 +35,7 @@ class MD_LE:
         self.ev_ff_strength = ev_ff_strength
         self.tolerance = tolerance
     
-    def run_pipeline(self,run_MD=True, friction=0.1, integrator_step=5 * mm.unit.femtosecond, sim_step=100, temperature=310, plots=False):
+    def run_pipeline(self,run_MD=True, friction=0.1, integrator_step=10 * mm.unit.femtosecond, sim_step=1000, ff_path = 'forcefields/classic_sm_ff.xml',temperature=310, plots=False):
         '''
         This is the basic function that runs the molecular simulation pipeline.
         '''
@@ -54,7 +54,7 @@ class MD_LE:
 
         # Define System
         pdb = PDBxFile(self.path+'/LE_init_struct.cif')
-        forcefield = ForceField('forcefields/classic_sm_ff.xml')
+        forcefield = ForceField(ff_path)
         self.system = forcefield.createSystem(pdb.topology, nonbondedCutoff=1*u.nanometer)
         integrator = mm.LangevinIntegrator(temperature, friction, integrator_step)
 

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/loopsage/plots.py

@@ -25,10 +25,6 @@ def make_loop_hist(Ms,Ns,path=None):
     if path!=None:
         save_path = path+'/plots/loop_length.png'
         plt.savefig(save_path,format='png',dpi=200)
-        save_path = path+'/plots/loop_length.svg'
-        plt.savefig(save_path,format='svg',dpi=600)
-        save_path = path+'/plots/loop_length.pdf'
-        plt.savefig(save_path,format='pdf',dpi=600)
     plt.close()
 
     Is, Js = Ms.flatten(), Ns.flatten()
@@ -40,10 +36,6 @@ def make_loop_hist(Ms,Ns,path=None):
     if path!=None:
         save_path = path+'/plots/ij_prob.png'
         plt.savefig(save_path,format='png',dpi=200)
-        save_path = path+'/plots/ij_prob.svg'
-        plt.savefig(save_path,format='svg',dpi=600)
-        save_path = path+'/plots/ij_prob.pdf'
-        plt.savefig(save_path,format='pdf',dpi=600)
     plt.close()
 
 def make_gif(N,path=None):
@@ -71,10 +63,6 @@ def make_timeplots(Es, Bs, Ks, Fs, burnin, mode, path=None):
     if path!=None:
         save_path = path+'/plots/energies.png'
         plt.savefig(save_path,format='png',dpi=200)
-        save_path = path+'/plots/energies.svg'
-        plt.savefig(save_path,format='svg',dpi=200)
-        save_path = path+'/plots/energies.pdf'
-        plt.savefig(save_path,format='pdf',dpi=600)
     plt.close()
 
     # Autocorrelation plot
@@ -91,10 +79,6 @@ def make_timeplots(Es, Bs, Ks, Fs, burnin, mode, path=None):
     if path!=None: 
         save_path = path+'/plots/autoc.png'
         plt.savefig(save_path,dpi=200)
-        save_path = path+'/plots/autoc.svg'
-        plt.savefig(save_path,format='svg',dpi=200)
-        save_path = path+'/plots/autoc.pdf'
-        plt.savefig(save_path,format='pdf',dpi=200)
     plt.close()
 
 def make_moveplots(unbinds, slides, path=None):
@@ -108,9 +92,7 @@ def make_moveplots(unbinds, slides, path=None):
     plt.grid()
     if path!=None:
         save_path = path+'/plots/moveplot.png'
-        plt.savefig(save_path,dpi=600)
-        save_path = path+'/plots/moveplot.pdf'
-        plt.savefig(save_path,dpi=600)
+        plt.savefig(save_path,dpi=200)
     plt.close()
 
 def average_pooling(mat,dim_new):
@@ -171,10 +153,6 @@ def coh_traj_plot(ms,ns,N_beads,path):
     plt.gca().invert_yaxis()
     save_path = path+'/plots/coh_trajectories.png' if path!=None else 'coh_trajectories.png'
     plt.savefig(save_path, format='png', dpi=200)
-    save_path = path+'/plots/coh_trajectories.svg' if path!=None else 'coh_trajectories.svg'
-    plt.savefig(save_path, format='svg', dpi=600)
-    save_path = path+'/plots/coh_trajectories.pdf' if path!=None else 'coh_trajectories.pdf'
-    plt.savefig(save_path, format='pdf', dpi=600)
     plt.close()
 
 def coh_probdist_plot(ms,ns,N_beads,path):
@@ -192,10 +170,6 @@ def coh_probdist_plot(ms,ns,N_beads,path):
     plt.title('Probablity distribution of cohesin')
     save_path = path+'/plots/coh_probdist.png' if path!=None else 'coh_trajectories.png'
     plt.savefig(save_path, format='png', dpi=200)
-    save_path = path+'/plots/coh_probdist.svg' if path!=None else 'coh_trajectories.svg'
-    plt.savefig(save_path, format='svg', dpi=600)
-    save_path = path+'/plots/coh_probdist.pdf' if path!=None else 'coh_trajectories.pdf'
-    plt.savefig(save_path, format='pdf', dpi=600)
     plt.close()
 
 def stochastic_heatmap(ms,ns,step,L,path,comm_prop=True,fill_square=True):
@@ -229,9 +203,7 @@ def stochastic_heatmap(ms,ns,step,L,path,comm_prop=True,fill_square=True):
     figure(figsize=(10, 10))
     plt.imshow(avg_mat,cmap="Reds",vmax=np.average(avg_mat)+3*np.std(avg_mat))
     save_path = path+f'/plots/stochastic_heatmap.svg' if path!=None else 'stochastic_heatmap.svg'
-    plt.savefig(save_path,format='svg',dpi=500)
-    save_path = path+f'/plots/stochastic_heatmap.pdf' if path!=None else 'stochastic_heatmap.pdf'
-    plt.savefig(save_path,format='pdf',dpi=500)
+    plt.savefig(save_path,format='svg',dpi=200)
     # plt.colorbar()
     plt.close()
 
@@ -266,8 +238,5 @@ def combine_matrices(path_upper,path_lower,label_upper,label_lower,th1=0,th2=50,
     # plt.ylabel('Genomic Distance (x5kb)',fontsize=16)
     plt.xlabel('Genomic Distance (x5kb)',fontsize=20)
     plt.ylabel('Genomic Distance (x5kb)',fontsize=20)
-    # plt.title('Experimental (upper triangle) versus simulation (lower triangle) heatmap',fontsize=25)
-    plt.savefig('comparison_reg3.svg',format='svg',dpi=500)
-    plt.savefig('comparison_reg3.png',format='png',dpi=500)
-    plt.savefig('comparison_reg3.pdf',format='pdf',dpi=500)
+    plt.savefig('comparison_reg3.png',format='png',dpi=200)
     plt.close()

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/loopsage/run.py

@@ -72,9 +72,9 @@ def main():
     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=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,args.VIZ_HEATS)
+        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,args.FORCEFIELD_PATH)
     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,args.VIZ_HEATS)
+        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,args.FORCEFIELD_PATH)
     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-1.0.9 → pyloopsage-1.0.11}/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,save_plots=True):
+    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,ff_path='forcefields/classic_sm_ff.xml'):
         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=save_plots,friction=friction,integrator_step=integrator_step,temperature=temperature)
+        sim_heat = em.run_pipeline(plots=save_plots,friction=friction,integrator_step=integrator_step,temperature=temperature,ff_path=ff_path)
         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,save_plots=True):
+    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,ff_path='forcefields/classic_sm_ff.xml'):
         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=save_plots,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,ff_path=ff_path)
         corr_exp_heat(sim_heat,self.bedpe_file,self.region,self.chrom,self.N_beads,self.path)
 
 def main():

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/pyLoopSage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.9
+Version: 1.0.11
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.9 → pyloopsage-1.0.11}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='1.0.9',  # Version of the software
+    version='1.0.11',  # 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',