PyPI - pyLoopSage - Versions diffs - 1.0.23__tar.gz → 1.1.0__tar.gz - Mend

pyLoopSage 1.0.23tar.gz → 1.1.0tar.gz

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{pyloopsage-1.0.23/pyLoopSage.egg-info → pyloopsage-1.1.0}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLoopSage
-Version: 1.0.23
+Version: 1.1.0
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -31,6 +31,7 @@ Requires-Dist: statsmodels
 Requires-Dist: imageio
 Requires-Dist: imageio[ffmpeg]
 Requires-Dist: pillow
+Requires-Dist: pyBigWig
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -271,35 +272,54 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 ### Long-table of LoopSage arguments
+#### General Settings
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |
 |------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | PLATFORM              | Name of the platform. Available choices: CPU, CUDA, OpenCL                                                      | str        | CPU               |
 | DEVICE                | Device index for CUDA or OpenCL (count from 0)                                                                  | str        | None                  |
-| N_BEADS               | Number of Simulation Beads.                                                                                     | int        | None                  |
-| BEDPE_PATH            | A .bedpe file path with loops. It is required.                                                                  | str        | None                  |
 | OUT_PATH              | Output folder name.                                                                                             | str        | ../results       |
+| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
+#### Input Data
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| BEDPE_PATH            | A .bedpe file path with loops. It is required.                                                                  | str        | None                  |
+| LEF_TRACK_FILE        | Path to a bw file of cohesin or condensin density. If it is provided, then simulation LEFs preferentially bind in enriched regions. | str | None |
+| BW_FILES              | List of paths to .bw files containing additional data for simulation. Enriched regions would act as barriers for cohesin.                | list       | None                  |
 | REGION_START          | Starting region coordinate.                                                                                     | int        | None                  |
 | REGION_END            | Ending region coordinate.                                                                                       | int        | None                  |
 | CHROM                 | Chromosome that corresponds to the modeling region of interest.                                                 | str        | None                  |
-| LEF_RW                | True if cohesins slide as a random walk instead of one direction.                                               | bool       | True                |
-| LEF_DRIFT             | True if LEFs are pushed back when they encounter other LEFs.                                                   | bool       | False               |
+#### Stochastic Simulation Parameters
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| N_BEADS               | Number of Simulation Beads.                                                                                     | int        | None                  |
 | N_STEPS               | Number of Monte Carlo steps.                                                                                    | int        | 40000               |
-| N_LEF                 | Number of loop extrusion factors.                                                                               | int        | None                  |
-| N_LEF2                | Number of second family loop extrusion factors.                                                                | int        | 0                   |
 | MC_STEP               | Monte Carlo frequency to avoid autocorrelated ensembles.                                                       | int        | 200                 |
 | BURNIN               | Burn-in period (steps before equilibrium).                                                                      | int        | 1000                |
 | T_INIT                | Initial Temperature of the Stochastic Model.                                                                   | float      | 2.0                 |
 | T_FINAL               | Final Temperature of the Stochastic Model.                                                                     | float      | 1.0                 |
 | METHOD                | Stochastic modeling method (Metropolis or Simulated Annealing).                                                | str        | 'Annealing'         |
+| LEF_RW                | True if cohesins slide as a random walk instead of one direction.                                               | bool       | True                |
+| LEF_DRIFT             | True if LEFs are pushed back when they encounter other LEFs.                                                   | bool       | False               |
+| N_LEF                 | Number of loop extrusion factors.                                                                               | int        | None                  |
+| N_LEF2                | Number of second family loop extrusion factors.                                                                | int        | 0                   |
+#### Energy Coefficients
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | FOLDING_COEFF         | Folding coefficient.                                                                                           | float      | 1.0                 |
 | FOLDING_COEFF2        | Folding coefficient for the second family of LEFs.                                                            | float      | 0.0                 |
 | CROSS_COEFF          | LEF crossing coefficient.                                                                                      | float      | 1.0                 |
 | CROSS_LOOP           | True if the penalty is applied when mi<mj<ni<nj. False if it applies only when mj=ni. When false it is better to enable LEF_DRIFT as well. | bool |True                |
 | BIND_COEFF           | CTCF binding coefficient.                                                                                      | float      | 1.0                 |
-| SAVE_PLOTS           | True to save diagnostic plots.                                                                                 | bool       | True                |
-| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
-| INITIAL_STRUCTURE_TYPE | Choose from: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.                                | str        | rw                |
+| BW_STRENGTHS          | List of strengths corresponding to each .bw file.                                                              | list       | None                  |
+#### Molecular Dynamics Simulation
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | SIMULATION_TYPE       | Either EM (energy minimizations) or MD (molecular dynamics).                                                  | str        | None                  |
+| INITIAL_STRUCTURE_TYPE | Choose from: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.                                | str        | rw                |
 | INTEGRATOR_STEP       | Step of the integrator.                                                                                        | Quantity   | 100 femtosecond   |
 | FORCEFIELD_PATH       | Path to XML file with forcefield.                                                                             | str        | default_xml_path    |
 | ANGLE_FF_STRENGTH     | Angle force strength.                                                                                          | float      | 200.0               |
@@ -311,10 +331,14 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 | EV_FF_POWER          | Excluded-volume power.                                                                                        | float      | 3.0                 |
 | FRICTION             | Friction coefficient of the Langevin integrator.                                                              | float      | 0.1              |
 | TOLERANCE            | Stopping condition for energy minimization.     | float      | 0.001              |
-| VIZ_HEATS            | True to visualize the output average heatmap.                                                                | bool       | True                |
 | SIM_TEMP             | Temperature of the 3D simulation (EM or MD).                                                                  | Quantity   | 310 kelvin        |
 | SIM_STEP             | Amount of simulation steps for loop force adjustments.                                                        | int        | 1000                |
+#### Visualization
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| VIZ_HEATS            | True to visualize the output average heatmap.                                                                | bool       | True                |
+| SAVE_PLOTS           | True to save diagnostic plots.                                                                                 | bool       | True                |
 ## Citation
 Please cite the method and biological paper in case that you would like to use this model for your work,

{pyloopsage-1.0.23 → pyloopsage-1.1.0}/README.md RENAMED Viewed

@@ -226,35 +226,54 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 ### Long-table of LoopSage arguments
+#### General Settings
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |
 |------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | PLATFORM              | Name of the platform. Available choices: CPU, CUDA, OpenCL                                                      | str        | CPU               |
 | DEVICE                | Device index for CUDA or OpenCL (count from 0)                                                                  | str        | None                  |
-| N_BEADS               | Number of Simulation Beads.                                                                                     | int        | None                  |
-| BEDPE_PATH            | A .bedpe file path with loops. It is required.                                                                  | str        | None                  |
 | OUT_PATH              | Output folder name.                                                                                             | str        | ../results       |
+| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
+#### Input Data
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| BEDPE_PATH            | A .bedpe file path with loops. It is required.                                                                  | str        | None                  |
+| LEF_TRACK_FILE        | Path to a bw file of cohesin or condensin density. If it is provided, then simulation LEFs preferentially bind in enriched regions. | str | None |
+| BW_FILES              | List of paths to .bw files containing additional data for simulation. Enriched regions would act as barriers for cohesin.                | list       | None                  |
 | REGION_START          | Starting region coordinate.                                                                                     | int        | None                  |
 | REGION_END            | Ending region coordinate.                                                                                       | int        | None                  |
 | CHROM                 | Chromosome that corresponds to the modeling region of interest.                                                 | str        | None                  |
-| LEF_RW                | True if cohesins slide as a random walk instead of one direction.                                               | bool       | True                |
-| LEF_DRIFT             | True if LEFs are pushed back when they encounter other LEFs.                                                   | bool       | False               |
+#### Stochastic Simulation Parameters
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| N_BEADS               | Number of Simulation Beads.                                                                                     | int        | None                  |
 | N_STEPS               | Number of Monte Carlo steps.                                                                                    | int        | 40000               |
-| N_LEF                 | Number of loop extrusion factors.                                                                               | int        | None                  |
-| N_LEF2                | Number of second family loop extrusion factors.                                                                | int        | 0                   |
 | MC_STEP               | Monte Carlo frequency to avoid autocorrelated ensembles.                                                       | int        | 200                 |
 | BURNIN               | Burn-in period (steps before equilibrium).                                                                      | int        | 1000                |
 | T_INIT                | Initial Temperature of the Stochastic Model.                                                                   | float      | 2.0                 |
 | T_FINAL               | Final Temperature of the Stochastic Model.                                                                     | float      | 1.0                 |
 | METHOD                | Stochastic modeling method (Metropolis or Simulated Annealing).                                                | str        | 'Annealing'         |
+| LEF_RW                | True if cohesins slide as a random walk instead of one direction.                                               | bool       | True                |
+| LEF_DRIFT             | True if LEFs are pushed back when they encounter other LEFs.                                                   | bool       | False               |
+| N_LEF                 | Number of loop extrusion factors.                                                                               | int        | None                  |
+| N_LEF2                | Number of second family loop extrusion factors.                                                                | int        | 0                   |
+#### Energy Coefficients
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | FOLDING_COEFF         | Folding coefficient.                                                                                           | float      | 1.0                 |
 | FOLDING_COEFF2        | Folding coefficient for the second family of LEFs.                                                            | float      | 0.0                 |
 | CROSS_COEFF          | LEF crossing coefficient.                                                                                      | float      | 1.0                 |
 | CROSS_LOOP           | True if the penalty is applied when mi<mj<ni<nj. False if it applies only when mj=ni. When false it is better to enable LEF_DRIFT as well. | bool |True                |
 | BIND_COEFF           | CTCF binding coefficient.                                                                                      | float      | 1.0                 |
-| SAVE_PLOTS           | True to save diagnostic plots.                                                                                 | bool       | True                |
-| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
-| INITIAL_STRUCTURE_TYPE | Choose from: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.                                | str        | rw                |
+| BW_STRENGTHS          | List of strengths corresponding to each .bw file.                                                              | list       | None                  |
+#### Molecular Dynamics Simulation
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | SIMULATION_TYPE       | Either EM (energy minimizations) or MD (molecular dynamics).                                                  | str        | None                  |
+| INITIAL_STRUCTURE_TYPE | Choose from: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.                                | str        | rw                |
 | INTEGRATOR_STEP       | Step of the integrator.                                                                                        | Quantity   | 100 femtosecond   |
 | FORCEFIELD_PATH       | Path to XML file with forcefield.                                                                             | str        | default_xml_path    |
 | ANGLE_FF_STRENGTH     | Angle force strength.                                                                                          | float      | 200.0               |
@@ -266,10 +285,14 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 | EV_FF_POWER          | Excluded-volume power.                                                                                        | float      | 3.0                 |
 | FRICTION             | Friction coefficient of the Langevin integrator.                                                              | float      | 0.1              |
 | TOLERANCE            | Stopping condition for energy minimization.     | float      | 0.001              |
-| VIZ_HEATS            | True to visualize the output average heatmap.                                                                | bool       | True                |
 | SIM_TEMP             | Temperature of the 3D simulation (EM or MD).                                                                  | Quantity   | 310 kelvin        |
 | SIM_STEP             | Amount of simulation steps for loop force adjustments.                                                        | int        | 1000                |
+#### Visualization
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| VIZ_HEATS            | True to visualize the output average heatmap.                                                                | bool       | True                |
+| SAVE_PLOTS           | True to save diagnostic plots.                                                                                 | bool       | True                |
 ## Citation
 Please cite the method and biological paper in case that you would like to use this model for your work,

{pyloopsage-1.0.23 → pyloopsage-1.1.0}/loopsage/__init__.py RENAMED Viewed

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
-__version__ = "1.0.23"
+__version__ = "1.1.0"

{pyloopsage-1.0.23 → pyloopsage-1.1.0}/loopsage/args_definition.py RENAMED Viewed

@@ -23,6 +23,7 @@ class Arg(object):
     type: type
     default: Union[str, float, int, bool, Quantity, None]
     val: Union[str, float, int, bool, Quantity, None]
+    nargs: Union[str, None] = None  # Optional attribute for nargs
 # Define custom type to parse list from string
 def parse_list(s):
@@ -65,6 +66,18 @@ class ListOfArgs(list):
             raise ValueError(f"I Can't recognise unit {unit} in expression {val}. Example of valid quantity: 12.3 femtosecond.")
         return Quantity(value=float(value), unit=unit)
+    def parse_list_of_floats(self, s: str) -> list:
+        try:
+            return [float(x.strip()) for x in s.strip('[]').split(',')]
+        except ValueError:
+            raise argparse.ArgumentTypeError("Invalid list format. Must be a comma-separated list of floats.")
+    def parse_list_of_strings(self, s: str) -> list:
+        try:
+            return [x.strip() for x in s.strip('[]').split(',')]
+        except ValueError:
+            raise argparse.ArgumentTypeError("Invalid list format. Must be a comma-separated list of strings.")
     def to_python(self):
         """Casts string args to ints, floats, bool..."""
         for i in self:
@@ -78,6 +91,22 @@ class ListOfArgs(list):
                 i.val = int(i.val)
             elif i.type == float:
                 i.val = float(i.val)
+            elif i.type == list:
+                if i.name == "BW_FILES" or i.name == "STRING_LIST":  # Handle lists of strings
+                    if isinstance(i.val, str):
+                        i.val = self.parse_list_of_strings(i.val)
+                    elif not isinstance(i.val, list):
+                        raise ValueError(f"Can't convert {i.val} into list of strings.")
+                elif i.name == "BW_STRENGTHS" or i.name == "FLOAT_LIST":  # Handle lists of floats
+                    if isinstance(i.val, str):
+                        i.val = self.parse_list_of_floats(i.val)
+                    elif not isinstance(i.val, list):
+                        raise ValueError(f"Can't convert {i.val} into list of floats.")
+                else:  # Handle lists of integers
+                    if isinstance(i.val, str):
+                        i.val = parse_list(i.val)
+                    elif not isinstance(i.val, list):
+                        raise ValueError(f"Can't convert {i.val} into list of integers.")
             elif i.type == bool:
                 if i.val.lower() in ['true', '1', 'y', 'yes']:
                     i.val = True
@@ -138,10 +167,14 @@ args = ListOfArgs([
     # Input data
     Arg('N_BEADS', help="Number of Simulation Beads.", type=int, default='', val=''),
     Arg('BEDPE_PATH', help="A .bedpe file path with loops. It is required.", type=str, default='', val=''),
+    Arg('LEF_TRACK_FILE', help="An optional track file for cohesin or condensin in bw format. If this file is specified LEF preferentially binds were the signal is enriched.", type=str, default='', val=''),
+    Arg('BW_FILES', help="List of bigWig file paths for feature extraction.", type=list, nargs='+', default=[], val=[]),
     Arg('OUT_PATH', help="Output folder name.", type=str, default='../results', val='../results'),
     Arg('REGION_START', help="Starting region coordinate.", type=int, default='', val=''),
     Arg('REGION_END', help="Ending region coordinate.", type=int, default='', val=''),
     Arg('CHROM', help="Chromosome that corresponds the the modelling region of interest (in case that you do not want to model the whole genome).", type=str, default='', val=''),
+    Arg('FLOAT_LIST', help="List of floating-point numbers.", type=list, nargs='+', default=[], val=[]),
+    Arg('STRING_LIST', help="List of strings.", type=list, nargs='+', default=[], val=[]),
     # 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'),
@@ -157,6 +190,7 @@ args = ListOfArgs([
     Arg('FOLDING_COEFF', help="Folding coefficient.", type=float, default='1.0', val='1.0'),
     Arg('FOLDING_COEFF2', help="Folding coefficient for the second family of LEFs.", type=float, default='0.0', val='0.0'),
     Arg('CROSS_COEFF', help="LEF crossing coefficient.", type=float, default='1.0', val='1.0'),
+    Arg('BW_STRENGTHS', help="List of strengths of the energy (floats) corresponding to each BW file. This equivalent to the `r` parameter in the LoopSage paper.", type=list, nargs='+', default=[], val=[]),
     Arg('CROSS_LOOP', help="It true if the penalty is applied for situations mi<mj<ni<nj and mi=nj, and false if it is applied only for mi=nj.", type=bool, default='True', val='True'),
     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'),

{pyloopsage-1.0.23 → pyloopsage-1.1.0}/loopsage/preproc.py RENAMED Viewed

@@ -2,7 +2,7 @@ import numpy as np
 import seaborn as sns
 import pandas as pd
 import matplotlib.pyplot as plt
-# import pyBigWig
+import pyBigWig
 from matplotlib.pyplot import figure
 def binding_vectors_from_bedpe(bedpe_file,N_beads,region,chrom,normalization=False,viz=False):
@@ -101,24 +101,24 @@ def get_rnap_energy(path,region,chrom,N_beads,normalization):
 def distance_point_line(x0,y0,a=1,b=-1,c=0):
     return np.abs(a*x0+b*y0+c)/np.sqrt(a**2+b**2)
-# def load_track(file,region,chrom,N_beads,viz=False,roll=False):
-#     bw = pyBigWig.open(file)
-#     weights = bw_to_array(bw, region, chrom, N_beads,viz,roll)
-#     return weights[:N_beads]
+def load_track(file,region,chrom,N_beads,viz=False,roll=False):
+    bw = pyBigWig.open(file)
+    weights = bw_to_array(bw, region, chrom, N_beads,viz,roll)
+    return weights[:N_beads]
-# def bw_to_array(bw, region, chrom, N_beads, viz=False, roll=False):
-#     step = (region[1]-region[0])//N_beads
-#     bw_array = bw.values(chrom, region[0], region[1])
-#     bw_array = np.nan_to_num(bw_array)
-#     bw_array_new = list()
-#     for i in range(step,len(bw_array)+1,step):
-#         bw_array_new.append(np.average(bw_array[(i-step):i]))
-#     weights = (np.roll(np.array(bw_array_new),3)+np.roll(np.array(bw_array_new),-3))/2 if roll else bw_array_new
-#     if viz:
-#         figure(figsize=(15, 5))
-#         plt.plot(weights)
-#         plt.grid()
-#         plt.title('ChIP-Seq signal',fontsize=20)
-#         plt.close()
+def bw_to_array(bw, region, chrom, N_beads, viz=False, roll=False):
+    step = (region[1]-region[0])//N_beads
+    bw_array = bw.values(chrom, region[0], region[1])
+    bw_array = np.nan_to_num(bw_array)
+    bw_array_new = list()
+    for i in range(step,len(bw_array)+1,step):
+        bw_array_new.append(np.average(bw_array[(i-step):i]))
+    weights = (np.roll(np.array(bw_array_new),3)+np.roll(np.array(bw_array_new),-3))/2 if roll else bw_array_new
+    if viz:
+        figure(figsize=(15, 5))
+        plt.plot(weights)
+        plt.grid()
+        plt.title('ChIP-Seq signal',fontsize=20)
+        plt.close()
-#     return weights
+    return weights

{pyloopsage-1.0.23 → pyloopsage-1.1.0}/loopsage/run.py RENAMED Viewed

@@ -69,9 +69,11 @@ def main():
     N_beads, N_lef, N_lef2 = args.N_BEADS, args.N_LEF, args.N_LEF2
     N_steps, MC_step, burnin, T, T_min = args.N_STEPS, args.MC_STEP, args.BURNIN, args.T_INIT, args.T_FINAL
     mode = args.METHOD
+    bw_paths = args.BW_FILES
     # Simulation Strengths
     f, f2, b, kappa = args.FOLDING_COEFF,  args.FOLDING_COEFF2, args.BIND_COEFF, args.CROSS_COEFF
+    r = args.BW_STRENGTHS
     # Definition of region
     region, chrom = [args.REGION_START,args.REGION_END], args.CHROM
@@ -81,12 +83,12 @@ def main():
     bedpe_file = args.BEDPE_PATH
     # Run Simulation
-    sim = StochasticSimulation(region,chrom,bedpe_file,out_dir=output_name,N_beads=N_beads,N_lef=N_lef,N_lef2=N_lef2)
-    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,f=f,f2=f2,b=b,kappa=kappa,lef_drift=args.LEF_DRIFT,cross_loop=args.CROSS_LOOP)
+    sim = StochasticSimulation(region,chrom,bedpe_file,out_dir=output_name,N_beads=N_beads,N_lef=N_lef,N_lef2=N_lef2, bw_files=bw_paths, track_file=args.LEF_TRACK_FILE)
+    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,f=f,f2=f2,b=b,kappa=kappa,lef_drift=args.LEF_DRIFT,cross_loop=args.CROSS_LOOP,r=r)
     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.EV_FF_POWER,args.TOLERANCE,args.FRICTION,args.INTEGRATOR_STEP,args.SIM_TEMP,args.INITIAL_STRUCTURE_TYPE,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.EV_FF_POWER,args.TOLERANCE,args.FRICTION,args.INTEGRATOR_STEP,args.SIM_TEMP,args.INITIAL_STRUCTURE_TYPE,args.SIM_STEP,args.VIZ_HEATS,args.FORCEFIELD_PATH,args.EV_P,args.CONTINUOUS_TOPOISOMERASE)
+        sim.run_MD(args.PLATFORM,args.ANGLE_FF_STRENGTH,args.LE_FF_LENGTH,args.LE_FF_STRENGTH,args.EV_FF_STRENGTH,args.EV_FF_POWER,args.TOLERANCE,args.FRICTION,args.INTEGRATOR_STEP,args.SIM_TEMP,args.INITIAL_STRUCTURE_TYPE,args.SIM_STEP,args.VIZ_HEATS,args.FORCEFIELD_PATH,args.EV_P,args.CONTINUOUS_TOP)
     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-1.0.23 → pyloopsage-1.1.0}/loopsage/stochastic_simulation.py RENAMED Viewed

@@ -66,12 +66,23 @@ def E_fold(ms, ns, fold_norm):
     return fold_norm * folding
 @njit
-def get_E(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, N_lef, N_lef2, cross_loop):
+def E_bw(N_bws, r, BWs, ms, ns):
+    '''
+    Calculation of the RNApII binding energy. Needs cohesins positions as input.
+    '''
+    E_bw = 0
+    for i in range(N_bws):
+        E_bw += r[i] * np.sum(BWs[i, ms] + BWs[i, ns]) / np.sum(BWs[i])
+    return E_bw
+@njit
+def get_E(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, N_lef, N_lef2, cross_loop, r=None, N_bws=0, BWs=None):
     ''''
     The total energy.
     '''
     energy = E_bind(L, R, ms, ns, bind_norm) + E_cross(ms, ns, k_norm, cross_loop) + E_fold(ms, ns, fold_norm)
     if fold_norm2!=0: energy += E_fold(ms[N_lef:N_lef+N_lef2],ns[N_lef:N_lef+N_lef2], fold_norm2)
+    if r is not None and BWs is not None: energy += E_bw(N_bws, r, BWs, ms, ns)
     return energy
 @njit
@@ -88,6 +99,13 @@ def get_dE_fold(fold_norm,ms,ns,m_new,n_new,idx):
     '''
     return fold_norm*(np.log(n_new-m_new)-np.log(ns[idx]-ms[idx]))
+@njit
+def get_dE_bw(N_bws, r, BWs, ms, ns, m_new, n_new, idx):
+    dE_bw = 0
+    for i in range(N_bws):
+        dE_bw += r[i] * (BWs[i, m_new] + BWs[i, n_new] - BWs[i, ms[idx]] - BWs[i, ns[idx]]) / np.sum(BWs[i])
+    return dE_bw
 @njit
 def get_dE_cross(ms, ns, m_new, n_new, idx, k_norm, cross_loop):
     '''
@@ -101,7 +119,7 @@ def get_dE_cross(ms, ns, m_new, n_new, idx, k_norm, cross_loop):
     return k_norm * (K2 - K1)
 @njit
-def get_dE(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, m_new, n_new, idx, N_lef, N_lef2, cross_loop):
+def get_dE(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, m_new, n_new, idx, N_lef, N_lef2, cross_loop, r=None, N_bws=0, BWs=None):
     '''
     Total energy difference.
     '''
@@ -112,14 +130,19 @@ def get_dE(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, m_new, n_new,
         dE += get_dE_fold(fold_norm2,ms[N_lef:N_lef+N_lef2],ns[N_lef:N_lef+N_lef2],m_new,n_new,idx-N_lef)
     dE += get_dE_bind(L, R, bind_norm, ms, ns, m_new, n_new, idx)
     dE += get_dE_cross(ms, ns, m_new, n_new, idx, k_norm, cross_loop)
+    if r is not None and BWs is not None: dE += get_dE_bw(N_bws, r, BWs, ms, ns, m_new, n_new, idx)
     return dE
 @njit
-def unbind_bind(N_beads):
+def unbind_bind(N_beads, track=None):
     '''
     Rebinding Monte-Carlo step.
     '''
-    m_new = rd.randint(0, N_beads - 3)
+    if track is not None:
+        weights = track / np.sum(track)
+        m_new = np.searchsorted(np.cumsum(weights), np.random.rand())
+    else:
+        m_new = np.random.randint(0, N_beads - 3)
     n_new = m_new + 2
     return int(m_new), int(n_new)
@@ -152,58 +175,58 @@ def unfolding_metric(ms,ns,N_beads):
     return unfold
 @njit
-def initialize(N_beads,N_lef):
+def initialize(N_beads, N_lef, track=None):
     '''
     Random initialization of polymer DNA fiber with some cohesin positions.
     '''
     ms, ns = np.zeros(N_lef,dtype=np.int64), np.zeros(N_lef,dtype=np.int64)
     for i in range(N_lef):
-        ms[i], ns[i] = unbind_bind(N_beads)
+        ms[i], ns[i] = unbind_bind(N_beads, track)
     return ms, ns
 @njit
-def run_simulation(N_beads,N_steps,MC_step,burnin,T,T_min,fold_norm,fold_norm2,bind_norm,k_norm,N_lef,N_lef2,L,R,mode,lef_rw=True,lef_drift=True,cross_loop=True):
+def run_simulation(N_beads, N_steps, MC_step, burnin, T, T_min, fold_norm, fold_norm2, bind_norm, k_norm, N_lef, N_lef2, L, R, mode, lef_rw=True, lef_drift=True, cross_loop=True, r=None, N_bws=0, BWs=None, track=None):
     '''
     Runs the Monte Carlo simulation.
     '''
     Ti = T
-    bi = burnin//MC_step
-    ms, ns = initialize(N_beads,N_lef+N_lef2)
-    E = get_E(L, R, bind_norm, fold_norm, fold_norm2, k_norm,  ms, ns, N_lef, N_lef2, cross_loop)
-    Es,Ks,Fs,Bs,ufs = np.zeros(N_steps//MC_step, dtype=np.float64),np.zeros(N_steps//MC_step, dtype=np.float64),np.zeros(N_steps//MC_step, dtype=np.float64),np.zeros(N_steps//MC_step, dtype=np.float64),np.zeros(N_steps//MC_step, dtype=np.float64)
-    Ms, Ns = np.zeros((N_lef+N_lef2,N_steps//MC_step), dtype=np.int64), np.zeros((N_lef+N_lef2,N_steps//MC_step), dtype=np.int64)
+    bi = burnin // MC_step
+    ms, ns = initialize(N_beads, N_lef + N_lef2, track)
+    E = get_E(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, N_lef, N_lef2, cross_loop, r, N_bws, BWs)
+    Es, Ks, Fs, Bs, ufs = np.zeros(N_steps // MC_step, dtype=np.float64), np.zeros(N_steps // MC_step, dtype=np.float64), np.zeros(N_steps // MC_step, dtype=np.float64), np.zeros(N_steps // MC_step, dtype=np.float64), np.zeros(N_steps // MC_step, dtype=np.float64)
+    Ms, Ns = np.zeros((N_lef + N_lef2, N_steps // MC_step), dtype=np.int64), np.zeros((N_lef + N_lef2, N_steps // MC_step), dtype=np.int64)
     for i in range(N_steps):
-        Ti = T-(T-T_min)*(i+1)/N_steps if mode=='Annealing' else T
-        for j in range(N_lef+N_lef2):
+        Ti = T - (T - T_min) * (i + 1) / N_steps if mode == 'Annealing' else T
+        for j in range(N_lef + N_lef2):
             # Randomly choose a move (sliding or rebinding)
-            r = np.random.choice(np.array([0, 1]))
-            if r==0:
-                m_new, n_new = unbind_bind(N_beads)
+            r_move = np.random.choice(np.array([0, 1]))
+            if r_move == 0:
+                m_new, n_new = unbind_bind(N_beads, track)
             else:
-                m_new, n_new = slide(ms[j],ns[j],ms,ns,N_beads,lef_rw,lef_drift)
+                m_new, n_new = slide(ms[j], ns[j], ms, ns, N_beads, lef_rw, lef_drift)
             # Compute energy difference
-            dE = get_dE(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, m_new, n_new, j, N_lef, N_lef2, cross_loop)
+            dE = get_dE(L, R, bind_norm, fold_norm, fold_norm2, k_norm, ms, ns, m_new, n_new, j, N_lef, N_lef2, cross_loop, r, N_bws, BWs)
-            if dE <= 0 or np.exp(-dE/Ti) > np.random.rand():
+            if dE <= 0 or np.exp(-dE / Ti) > np.random.rand():
                 ms[j], ns[j] = m_new, n_new
                 E += dE
             # Compute Metrics
-            if i%MC_step==0:
-                Ms[j,i//MC_step], Ns[j,i//MC_step] = ms[j], ns[j]
+            if i % MC_step == 0:
+                Ms[j, i // MC_step], Ns[j, i // MC_step] = ms[j], ns[j]
         # Compute Metrics
-        if i%MC_step==0:
-            ufs[i//MC_step] = unfolding_metric(ms,ns,N_beads)
-            Es[i//MC_step] = E
-            Ks[i//MC_step] = E_cross(ms,ns,k_norm,cross_loop)
-            Fs[i//MC_step] = E_fold(ms,ns,fold_norm)
-            Bs[i//MC_step] = E_bind(L,R,ms,ns,bind_norm)
+        if i % MC_step == 0:
+            ufs[i // MC_step] = unfolding_metric(ms, ns, N_beads)
+            Es[i // MC_step] = E
+            Ks[i // MC_step] = E_cross(ms, ns, k_norm, cross_loop)
+            Fs[i // MC_step] = E_fold(ms, ns, fold_norm)
+            Bs[i // MC_step] = E_bind(L, R, ms, ns, bind_norm)
     return Ms, Ns, Es, Ks, Fs, Bs, ufs
 class StochasticSimulation:
-    def __init__(self,region,chrom,bedpe_file,N_beads=None,N_lef=None,N_lef2=0,out_dir=None):
+    def __init__(self,region,chrom,bedpe_file,N_beads=None,N_lef=None,N_lef2=0,out_dir=None, bw_files=None, track_file=None):
         '''
         Definition of simulation parameters and input files.
@@ -218,16 +241,17 @@ class StochasticSimulation:
         r (list): strength of each ChIP-Seq experinment.
         '''
         self.N_beads = N_beads if N_beads!=None else int(np.round((region[1]-region[0])/2000))
+        self.N_bws = len(bw_files) if bw_files else 0
         print('Number of beads:',self.N_beads)
         self.chrom, self.region = chrom, region
-        self.bedpe_file = bedpe_file
+        self.bedpe_file, self.bw_files, self.track_file = bedpe_file, bw_files, track_file
         self.preprocessing()
         self.N_lef = 2*self.N_CTCF if N_lef==None else N_lef
         self.N_lef2 = N_lef2
         print('Number of LEFs:',self.N_lef+self.N_lef2)
         self.path = make_folder(out_dir)
-    def run_energy_minimization(self,N_steps,MC_step,burnin,T=1,T_min=0,mode='Metropolis',viz=False,save=False, f=1.0, f2=0.0, b=1.0, kappa=1.0, lef_rw=True, lef_drift=True, cross_loop=True):
+    def run_energy_minimization(self, N_steps, MC_step, burnin, T=1, T_min=0, mode='Metropolis', viz=False, save=False, f=1.0, f2=0.0, b=1.0, kappa=1.0, lef_rw=True, lef_drift=True, cross_loop=True, r=None):
         '''
         Implementation of the stochastic Monte Carlo simulation.
@@ -238,19 +262,23 @@ class StochasticSimulation:
         T (float): simulation (initial) temperature.
         mode (str): it can be either 'Metropolis' or 'Annealing'.
         viz (bool): True in case that user wants to see plots.
+        r (list): strength of each ChIP-Seq experiment.
+        N_bws (int): number of binding weight matrices.
+        BWs (np.ndarray): binding weight matrices.
         '''
         # Define normalization constants
         fold_norm, fold_norm2, bind_norm, k_norm = -self.N_beads*f/((self.N_lef+self.N_lef2)*np.log(self.N_beads/(self.N_lef+self.N_lef2))), -self.N_beads*f2/((self.N_lef+self.N_lef2)*np.log(self.N_beads/(self.N_lef+self.N_lef2))), -self.N_beads*b/(np.sum(self.L)+np.sum(self.R)), kappa*1e4
         self.N_steps, self.MC_step = N_steps, MC_step
+        r = np.full(self.N_bws, -self.N_beads / 10) if not r and self.N_bws > 0 else (None if not r else r)
         # Run simulation
         print('\nRunning simulation (with parallelization across CPU cores)...')
         start = time.time()
         self.burnin = burnin
-        self.Ms, self.Ns, self.Es, self.Ks, self.Fs, self.Bs, self.ufs = run_simulation(self.N_beads,N_steps,MC_step,burnin,T,T_min,fold_norm,fold_norm2,bind_norm,k_norm,self.N_lef,self.N_lef2,self.L,self.R,mode,lef_rw,lef_drift,cross_loop)
+        self.Ms, self.Ns, self.Es, self.Ks, self.Fs, self.Bs, self.ufs = run_simulation(self.N_beads, N_steps, MC_step, burnin, T, T_min, fold_norm, fold_norm2, bind_norm, k_norm, self.N_lef, self.N_lef2, self.L, self.R, mode, lef_rw, lef_drift, cross_loop, r, self.N_bws, self.BWs, self.lef_track)
         end = time.time()
         elapsed = end - start
-        print(f'Computation finished succesfully in {elapsed//3600:.0f} hours, {elapsed%3600//60:.0f} minutes and  {elapsed%60:.0f} seconds.')
+        print(f'Computation finished successfully in {elapsed//3600:.0f} hours, {elapsed%3600//60:.0f} minutes and {elapsed%60:.0f} seconds.')
         # Save simulation info
         if save:
@@ -265,7 +293,9 @@ class StochasticSimulation:
                 file.write(f'Crossing energy in equilibrium is {np.average(self.Ks[burnin//MC_step:]):.2f}. Crossing coefficient kappa={kappa}.\n')
                 file.write(f'Folding energy in equilibrium is {np.average(self.Fs[burnin//MC_step:]):.2f}. Folding coefficient f={f}. Folding coefficient for the second family f2={f2}\n')
                 file.write(f'Binding energy in equilibrium is {np.average(self.Bs[burnin//MC_step:]):.2f}. Binding coefficient b={b}.\n')
-                file.write(f'Energy at equillibrium: {np.average(self.Es[self.burnin//MC_step:]):.2f}.\n')
+                if r is not None and self.BWs is not None:
+                    file.write(f'RNApII binding energy included with {N_bws} binding weight matrices.\n')
+                file.write(f'Energy at equilibrium: {np.average(self.Es[self.burnin//MC_step:]):.2f}.\n')
             np.save(save_dir + 'Ms.npy', self.Ms)
             np.save(save_dir + 'Ns.npy', self.Ns)
             np.save(save_dir + 'ufs.npy', self.ufs)
@@ -274,16 +304,27 @@ class StochasticSimulation:
             np.save(save_dir + 'Fs.npy', self.Fs)
             np.save(save_dir + 'Ks.npy', self.Ks)
-        # Some vizualizations
-        if viz: coh_traj_plot(self.Ms,self.Ns,self.N_beads, self.path)
+        # Some visualizations
+        if viz: coh_traj_plot(self.Ms, self.Ns, self.N_beads, self.path)
         if viz: make_timeplots(self.Es, self.Bs, self.Ks, self.Fs, burnin//MC_step, mode, self.path)
-        if viz: coh_probdist_plot(self.Ms,self.Ns,self.N_beads,self.path)
-        if viz and self.N_beads<=2000: stochastic_heatmap(self.Ms,self.Ns,MC_step,self.N_beads,self.path)
+        if viz: coh_probdist_plot(self.Ms, self.Ns, self.N_beads, self.path)
+        if viz and self.N_beads <= 2000: stochastic_heatmap(self.Ms, self.Ns, MC_step, self.N_beads, self.path)
         return self.Es, self.Ms, self.Ns, self.Bs, self.Ks, self.Fs, self.ufs
     def preprocessing(self):
         self.L, self.R, self.dists = binding_vectors_from_bedpe(self.bedpe_file,self.N_beads,self.region,self.chrom,False,False)
+        if not self.bw_files:
+            self.BWs = None
+            self.N_bws = 0
+        else:
+            if isinstance(self.bw_files, str):
+                self.bw_files = [self.bw_files]
+                self.N_bws = 1
+            self.BWs = np.zeros((self.N_bws, self.N_beads))
+            for i, f in enumerate(self.bw_files):
+                self.BWs[i, :] = load_track(file=f, region=self.region, chrom=self.chrom, N_beads=self.N_beads, viz=False)
+        self.lef_track = load_track(self.track_file,self.region,self.chrom,self.N_beads,False,True) if self.track_file else None
         self.N_CTCF = np.max([np.count_nonzero(self.L),np.count_nonzero(self.R)])
         print('Number of CTCF:',self.N_CTCF)
@@ -316,7 +357,7 @@ def main():
     sim = StochasticSimulation(region,chrom,bedpe_file,out_dir=output_name,N_beads=1000,N_lef=N_lef,N_lef2=N_lef2)
     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,f=f,f2=f2, b=b, kappa=kappa, lef_rw=lew_rw)
-    sim.run_MD('CUDA',continuous_topoisomerase=True, p_ev=0.1)
+    sim.run_MD('CUDA',continuous_topoisomerase=True, p_ev=0.01)
 if __name__=='__main__':
     main()

{pyloopsage-1.0.23 → pyloopsage-1.1.0/pyLoopSage.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLoopSage
-Version: 1.0.23
+Version: 1.1.0
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -31,6 +31,7 @@ Requires-Dist: statsmodels
 Requires-Dist: imageio
 Requires-Dist: imageio[ffmpeg]
 Requires-Dist: pillow
+Requires-Dist: pyBigWig
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -271,35 +272,54 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 ### Long-table of LoopSage arguments
+#### General Settings
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |
 |------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | PLATFORM              | Name of the platform. Available choices: CPU, CUDA, OpenCL                                                      | str        | CPU               |
 | DEVICE                | Device index for CUDA or OpenCL (count from 0)                                                                  | str        | None                  |
-| N_BEADS               | Number of Simulation Beads.                                                                                     | int        | None                  |
-| BEDPE_PATH            | A .bedpe file path with loops. It is required.                                                                  | str        | None                  |
 | OUT_PATH              | Output folder name.                                                                                             | str        | ../results       |
+| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
+#### Input Data
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| BEDPE_PATH            | A .bedpe file path with loops. It is required.                                                                  | str        | None                  |
+| LEF_TRACK_FILE        | Path to a bw file of cohesin or condensin density. If it is provided, then simulation LEFs preferentially bind in enriched regions. | str | None |
+| BW_FILES              | List of paths to .bw files containing additional data for simulation. Enriched regions would act as barriers for cohesin.                | list       | None                  |
 | REGION_START          | Starting region coordinate.                                                                                     | int        | None                  |
 | REGION_END            | Ending region coordinate.                                                                                       | int        | None                  |
 | CHROM                 | Chromosome that corresponds to the modeling region of interest.                                                 | str        | None                  |
-| LEF_RW                | True if cohesins slide as a random walk instead of one direction.                                               | bool       | True                |
-| LEF_DRIFT             | True if LEFs are pushed back when they encounter other LEFs.                                                   | bool       | False               |
+#### Stochastic Simulation Parameters
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| N_BEADS               | Number of Simulation Beads.                                                                                     | int        | None                  |
 | N_STEPS               | Number of Monte Carlo steps.                                                                                    | int        | 40000               |
-| N_LEF                 | Number of loop extrusion factors.                                                                               | int        | None                  |
-| N_LEF2                | Number of second family loop extrusion factors.                                                                | int        | 0                   |
 | MC_STEP               | Monte Carlo frequency to avoid autocorrelated ensembles.                                                       | int        | 200                 |
 | BURNIN               | Burn-in period (steps before equilibrium).                                                                      | int        | 1000                |
 | T_INIT                | Initial Temperature of the Stochastic Model.                                                                   | float      | 2.0                 |
 | T_FINAL               | Final Temperature of the Stochastic Model.                                                                     | float      | 1.0                 |
 | METHOD                | Stochastic modeling method (Metropolis or Simulated Annealing).                                                | str        | 'Annealing'         |
+| LEF_RW                | True if cohesins slide as a random walk instead of one direction.                                               | bool       | True                |
+| LEF_DRIFT             | True if LEFs are pushed back when they encounter other LEFs.                                                   | bool       | False               |
+| N_LEF                 | Number of loop extrusion factors.                                                                               | int        | None                  |
+| N_LEF2                | Number of second family loop extrusion factors.                                                                | int        | 0                   |
+#### Energy Coefficients
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | FOLDING_COEFF         | Folding coefficient.                                                                                           | float      | 1.0                 |
 | FOLDING_COEFF2        | Folding coefficient for the second family of LEFs.                                                            | float      | 0.0                 |
 | CROSS_COEFF          | LEF crossing coefficient.                                                                                      | float      | 1.0                 |
 | CROSS_LOOP           | True if the penalty is applied when mi<mj<ni<nj. False if it applies only when mj=ni. When false it is better to enable LEF_DRIFT as well. | bool |True                |
 | BIND_COEFF           | CTCF binding coefficient.                                                                                      | float      | 1.0                 |
-| SAVE_PLOTS           | True to save diagnostic plots.                                                                                 | bool       | True                |
-| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
-| INITIAL_STRUCTURE_TYPE | Choose from: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.                                | str        | rw                |
+| BW_STRENGTHS          | List of strengths corresponding to each .bw file.                                                              | list       | None                  |
+#### Molecular Dynamics Simulation
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
 | SIMULATION_TYPE       | Either EM (energy minimizations) or MD (molecular dynamics).                                                  | str        | None                  |
+| INITIAL_STRUCTURE_TYPE | Choose from: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.                                | str        | rw                |
 | INTEGRATOR_STEP       | Step of the integrator.                                                                                        | Quantity   | 100 femtosecond   |
 | FORCEFIELD_PATH       | Path to XML file with forcefield.                                                                             | str        | default_xml_path    |
 | ANGLE_FF_STRENGTH     | Angle force strength.                                                                                          | float      | 200.0               |
@@ -311,10 +331,14 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 | EV_FF_POWER          | Excluded-volume power.                                                                                        | float      | 3.0                 |
 | FRICTION             | Friction coefficient of the Langevin integrator.                                                              | float      | 0.1              |
 | TOLERANCE            | Stopping condition for energy minimization.     | float      | 0.001              |
-| VIZ_HEATS            | True to visualize the output average heatmap.                                                                | bool       | True                |
 | SIM_TEMP             | Temperature of the 3D simulation (EM or MD).                                                                  | Quantity   | 310 kelvin        |
 | SIM_STEP             | Amount of simulation steps for loop force adjustments.                                                        | int        | 1000                |
+#### Visualization
+| Argument Name          | Description                                                                                                     | Type        | Default Value       |
+|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
+| VIZ_HEATS            | True to visualize the output average heatmap.                                                                | bool       | True                |
+| SAVE_PLOTS           | True to save diagnostic plots.                                                                                 | bool       | True                |
 ## Citation
 Please cite the method and biological paper in case that you would like to use this model for your work,

{pyloopsage-1.0.23 → pyloopsage-1.1.0}/pyLoopSage.egg-info/requires.txt RENAMED Viewed

@@ -17,3 +17,4 @@ statsmodels
 imageio
 imageio[ffmpeg]
 pillow
+pyBigWig

{pyloopsage-1.0.23 → pyloopsage-1.1.0}/setup.py RENAMED Viewed

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 setup(
     name='pyLoopSage',  # Package name
-    version='1.0.23',  # Version of the software
+    version='1.1.0',  # 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',
@@ -39,6 +39,7 @@ setup(
         'imageio',
         'imageio[ffmpeg]',
         'pillow',
+        'pyBigWig',
     ],
     entry_points={
         'console_scripts': [