pyLoopSage 1.1.6__tar.gz → 1.1.7__tar.gz

{pyloopsage-1.1.6/pyLoopSage.egg-info → pyloopsage-1.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLoopSage
-Version: 1.1.6
+Version: 1.1.7
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -48,7 +48,7 @@ Dynamic: summary
 # pyLoopSage
 Updated version of the stochastic loop extrusion model: LoopSage with capability to run incredibly fast, parallelized across CPU cores. This package is even more user-friendly and it can be installed via PyPI.
 
-<img width="1774" height="887" alt="image" src="https://github.com/user-attachments/assets/7c338772-9fd5-4b57-8965-65d346b7f11c" />
+![screenshot](https://github.com/user-attachments/assets/7c338772-9fd5-4b57-8965-65d346b7f11c)
 
 ## New features
 
@@ -82,7 +82,7 @@ $K(m_{i},n_{i};m_{j},n_{j})$ which takes the value 1 when $m_{i} < m_{j} < n_{i}
 
 These $L(\cdot), R(\cdot)$ functions are two functions that define the binding potential and they are orientation specific - so they are different for left and right position of cohesin (because CTCF motifs are orientation specific), therefore when we have a gap in these functions, it means presence of CTCF. These two functions are derived from data with CTCF binning and by running the script for probabilistic orientation. Moreover, by $N_{(\cdot)}$ we symbolize the normalization constants for each factor,
 
-$$c_{\text{fold}}=-\dfrac{N_{\text{beads}}f}{N_{\text{lef}}\log(N_{\text{beads}}/N_{\text{lef}})},\quad c_{\text{bind}}=-\dfrac{N_{\text{beads}}b}{\sum_i \left(L(m_i)+R(n_i)\right)},\quad c_{\text{cross}}=\kappa \times 10^4.$$
+$$c_{\text{fold}}=-\dfrac{N_{\text{beads}}f}{N_{\text{lef}}\log(N_{\text{beads}}/N_{\text{lef}})},\quad c_{\text{bind}}=-\dfrac{2N_{\text{beads}}b}{N_{CTCF}},\quad c_{\text{cross}}=\kappa \times 10^4.$$
 
 The parameters are defined in such a way that when $f=b=\kappa=1$, the three terms of the stochastic energy are balanced. To clarrify, this parametrization is slightly different than this of the original paper. We multiply with $N_{\text{beads}}$, so as to keep the input parameters $f,b,\kappa$ simpler close to 1. Therefore, a value $f=0.1$ leads to unfolded structures, and a value $f=2$ it leads to very fast propagating long loops. 
 
@@ -341,40 +341,47 @@ 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                  |
-| OUT_PATH              | Output folder name.                                                                                             | str        | ../results       |
-| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
+| Argument | Description | Type | Default |
+|---|---|---|---|
+| PLATFORM | Simulation platform: CPU, CUDA, or OpenCL | str | CPU |
+| DEVICE | CUDA/OpenCL device index (from 0) | str | None |
+| OUT_PATH | Output folder path | str | ../results |
+| SAVE_MDT | Save simulation metadata | bool | True |
 
 #### Input Data
-| Argument Name          | Description                                                                                                     | Type        | Default Value       |
-|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
-| INTERACTION_FILE      | A .bedpe, .bed or .narrowPeaks input file. 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                  |
-| GENOME                | Reference genome assembly used to define chromosome sizes and genomic coordinates (e.g., hg19 or hg38).         | str        | hg38                  |
+| Argument | Description | Type | Default |
+|---|---|---|---|
+| INTERACTION_FILE | Loop/peak file (.bedpe, .bed, or .narrowPeak). Required. | str | None |
+| LEF_TRACK_FILE | bigWig track biasing LEF loading toward enriched regions | str | None |
+| BW_FILES | bigWig file(s) acting as extrusion barriers | list | None |
+| SMOOTHING_INPUT | Smooth noisy/sparse loop-peak signal before use | bool | False |
+| COMP_BW_FILE | bigWig track for A/B compartment bias | str | None |
+| COMP_BED_FILE | BED file for A/B compartment bias (alt. to COMP_BW_FILE) | str | None |
+| DATA_LOSS_MODE | 0 = 1D binding potentials (L/R); 1 = 2D loss interpolated from input loops | int | 0 |
+| CONTRASTIVE_BINDING | If True, penalizes loop-free regions so extrusion is confined within TADs; if False, extrusion is uniform everywhere | bool | False |
+| REGION_START | Region start coordinate | int | None |
+| REGION_END | Region end coordinate | int | None |
+| CHROM | Chromosome of the modeled region | str | None |
+| GENOME | Reference genome for chromosome sizes (e.g. hg38) | str | hg38 |
+| FLOAT_LIST | Extra custom numeric settings | list | None |
+| STRING_LIST | Extra custom text settings | list | None |
 
 #### 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               |
-| 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                   |
-| 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                |
-| BETWEEN_FAMILIES_PENALTY | Penalty applied when loops from different LEF families cross.                                                | bool     | True                 |
+| Argument | Description | Type | Default |
+|---|---|---|---|
+| N_BEADS | Number of simulation beads | int | None |
+| N_STEPS | Monte Carlo steps | int | 40000 |
+| MC_STEP | Sampling frequency (reduces autocorrelation) | int | 200 |
+| BURNIN | Steps discarded before equilibrium | int | 1000 |
+| T_INIT | Initial temperature | float | 2.0 |
+| T_FINAL | Final temperature | float | 1.0 |
+| METHOD | 'Metropolis' or 'Annealing' | str | 'Annealing' |
+| LEF_RW | Cohesins slide as random walk (vs. one direction) | bool | True |
+| LEF_DRIFT | LEFs bounce back off each other | bool | False |
+| N_LEF | Number of loop extrusion factors | int | None |
+| N_LEF2 | Number of second-family LEFs | int | 0 |
+| CROSS_LOOP | Penalize mi<mj<ni<nj crossings (vs. only mj=ni); pair with LEF_DRIFT if False | bool | True |
+| BETWEEN_FAMILIES_PENALTY | Penalize crossings between LEF families | bool | True |
 
 #### Energy Coefficients
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |

{pyloopsage-1.1.6 → pyloopsage-1.1.7}/README.md

@@ -1,7 +1,7 @@
 # pyLoopSage
 Updated version of the stochastic loop extrusion model: LoopSage with capability to run incredibly fast, parallelized across CPU cores. This package is even more user-friendly and it can be installed via PyPI.
 
-<img width="1774" height="887" alt="image" src="https://github.com/user-attachments/assets/7c338772-9fd5-4b57-8965-65d346b7f11c" />
+![screenshot](https://github.com/user-attachments/assets/7c338772-9fd5-4b57-8965-65d346b7f11c)
 
 ## New features
 
@@ -35,7 +35,7 @@ $K(m_{i},n_{i};m_{j},n_{j})$ which takes the value 1 when $m_{i} < m_{j} < n_{i}
 
 These $L(\cdot), R(\cdot)$ functions are two functions that define the binding potential and they are orientation specific - so they are different for left and right position of cohesin (because CTCF motifs are orientation specific), therefore when we have a gap in these functions, it means presence of CTCF. These two functions are derived from data with CTCF binning and by running the script for probabilistic orientation. Moreover, by $N_{(\cdot)}$ we symbolize the normalization constants for each factor,
 
-$$c_{\text{fold}}=-\dfrac{N_{\text{beads}}f}{N_{\text{lef}}\log(N_{\text{beads}}/N_{\text{lef}})},\quad c_{\text{bind}}=-\dfrac{N_{\text{beads}}b}{\sum_i \left(L(m_i)+R(n_i)\right)},\quad c_{\text{cross}}=\kappa \times 10^4.$$
+$$c_{\text{fold}}=-\dfrac{N_{\text{beads}}f}{N_{\text{lef}}\log(N_{\text{beads}}/N_{\text{lef}})},\quad c_{\text{bind}}=-\dfrac{2N_{\text{beads}}b}{N_{CTCF}},\quad c_{\text{cross}}=\kappa \times 10^4.$$
 
 The parameters are defined in such a way that when $f=b=\kappa=1$, the three terms of the stochastic energy are balanced. To clarrify, this parametrization is slightly different than this of the original paper. We multiply with $N_{\text{beads}}$, so as to keep the input parameters $f,b,\kappa$ simpler close to 1. Therefore, a value $f=0.1$ leads to unfolded structures, and a value $f=2$ it leads to very fast propagating long loops. 
 
@@ -294,40 +294,47 @@ 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                  |
-| OUT_PATH              | Output folder name.                                                                                             | str        | ../results       |
-| SAVE_MDT             | True to save metadata of the stochastic simulation.                                                            | bool       | True                |
+| Argument | Description | Type | Default |
+|---|---|---|---|
+| PLATFORM | Simulation platform: CPU, CUDA, or OpenCL | str | CPU |
+| DEVICE | CUDA/OpenCL device index (from 0) | str | None |
+| OUT_PATH | Output folder path | str | ../results |
+| SAVE_MDT | Save simulation metadata | bool | True |
 
 #### Input Data
-| Argument Name          | Description                                                                                                     | Type        | Default Value       |
-|------------------------|-----------------------------------------------------------------------------------------------------------------|------------|---------------------|
-| INTERACTION_FILE      | A .bedpe, .bed or .narrowPeaks input file. 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                  |
-| GENOME                | Reference genome assembly used to define chromosome sizes and genomic coordinates (e.g., hg19 or hg38).         | str        | hg38                  |
+| Argument | Description | Type | Default |
+|---|---|---|---|
+| INTERACTION_FILE | Loop/peak file (.bedpe, .bed, or .narrowPeak). Required. | str | None |
+| LEF_TRACK_FILE | bigWig track biasing LEF loading toward enriched regions | str | None |
+| BW_FILES | bigWig file(s) acting as extrusion barriers | list | None |
+| SMOOTHING_INPUT | Smooth noisy/sparse loop-peak signal before use | bool | False |
+| COMP_BW_FILE | bigWig track for A/B compartment bias | str | None |
+| COMP_BED_FILE | BED file for A/B compartment bias (alt. to COMP_BW_FILE) | str | None |
+| DATA_LOSS_MODE | 0 = 1D binding potentials (L/R); 1 = 2D loss interpolated from input loops | int | 0 |
+| CONTRASTIVE_BINDING | If True, penalizes loop-free regions so extrusion is confined within TADs; if False, extrusion is uniform everywhere | bool | False |
+| REGION_START | Region start coordinate | int | None |
+| REGION_END | Region end coordinate | int | None |
+| CHROM | Chromosome of the modeled region | str | None |
+| GENOME | Reference genome for chromosome sizes (e.g. hg38) | str | hg38 |
+| FLOAT_LIST | Extra custom numeric settings | list | None |
+| STRING_LIST | Extra custom text settings | list | None |
 
 #### 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               |
-| 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                   |
-| 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                |
-| BETWEEN_FAMILIES_PENALTY | Penalty applied when loops from different LEF families cross.                                                | bool     | True                 |
+| Argument | Description | Type | Default |
+|---|---|---|---|
+| N_BEADS | Number of simulation beads | int | None |
+| N_STEPS | Monte Carlo steps | int | 40000 |
+| MC_STEP | Sampling frequency (reduces autocorrelation) | int | 200 |
+| BURNIN | Steps discarded before equilibrium | int | 1000 |
+| T_INIT | Initial temperature | float | 2.0 |
+| T_FINAL | Final temperature | float | 1.0 |
+| METHOD | 'Metropolis' or 'Annealing' | str | 'Annealing' |
+| LEF_RW | Cohesins slide as random walk (vs. one direction) | bool | True |
+| LEF_DRIFT | LEFs bounce back off each other | bool | False |
+| N_LEF | Number of loop extrusion factors | int | None |
+| N_LEF2 | Number of second-family LEFs | int | 0 |
+| CROSS_LOOP | Penalize mi<mj<ni<nj crossings (vs. only mj=ni); pair with LEF_DRIFT if False | bool | True |
+| BETWEEN_FAMILIES_PENALTY | Penalize crossings between LEF families | bool | True |
 
 #### Energy Coefficients
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |

{pyloopsage-1.1.6 → pyloopsage-1.1.7}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.1.6"
+__version__ = "1.1.7"

{pyloopsage-1.1.6 → pyloopsage-1.1.7}/loopsage/args_definition.py

@@ -172,6 +172,7 @@ args = ListOfArgs([
     Arg('INTERACTION_FILE', help="A .bedpe, .bed, or .narrowPeak 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('SMOOTHING_INPUT',help="Determines if the input signal from peaks or anchros, will be smoothed.", type=bool, default='False', val='False'),
     Arg('COMP_BW_FILE', help="A bw file for compartmentalization. ", type=str,  default='', val=''),
     Arg('COMP_BED_FILE', help="A bed file for compartmentalization. ", type=str,  default='', val=''),
     Arg('OUT_PATH', help="Output folder name.", type=str, default='../results', val='../results'),

{pyloopsage-1.1.6 → pyloopsage-1.1.7}/loopsage/preproc.py

@@ -46,7 +46,7 @@ def binding_vectors_from_bedpe(
         diagonal_interactions=True,
         alpha=1.0,
         smooth=False,
-        smooth_sigma=2.0,
+        smooth_sigma=1.0,
         contrastive=True
     ):
     '''
@@ -369,7 +369,7 @@ def binding_vectors_from_bedpe(
 
         plt.close()
 
-    return 2*L, 2*R, J, np.sqrt(len(loop_lengths))*J_loss, statistics
+    return L, R, J, np.sqrt(len(loop_lengths))*J_loss, statistics
 
 def _prepare_region(chrom, region):
     """Shared region-resolution logic (identical to binding_vectors_from_bedpe)."""
@@ -400,7 +400,7 @@ def _binding_vectors_from_single_region(
         diagonal_interactions=True,
         alpha=1.0,
         smooth=False,
-        smooth_sigma=2.0,
+        smooth_sigma=1.0,
         contrastive=True,
         source_label="peaks"
     ):
@@ -508,7 +508,7 @@ def _binding_vectors_from_single_region(
             plt.savefig(os.path.join(plot_dir, f"LR_profiles_{source_label}.pdf"), dpi=600, format="pdf")
         plt.close()
  
-    return 2 * L, 2 * R, J, J_loss, statistics
+    return L, R, J, J_loss, statistics
  
 def binding_vectors_from_bed(
         bed_file, N_beads, chrom, region=None, out_path=None,
@@ -517,7 +517,7 @@ def binding_vectors_from_bed(
         diagonal_interactions=True,
         alpha=1.0,
         smooth=False,
-        smooth_sigma=2.0,
+        smooth_sigma=1.0,
         contrastive=True
     ):
     '''
@@ -588,7 +588,7 @@ def binding_vectors_from_narrowpeak(
         diagonal_interactions=True,
         alpha=1.0,
         smooth=False,
-        smooth_sigma=2.0,
+        smooth_sigma=1.0,
         contrastive=True
     ):
     '''

{pyloopsage-1.1.6 → pyloopsage-1.1.7}/loopsage/run.py

@@ -177,7 +177,8 @@ def main():
         lef_density_file=args.LEF_TRACK_FILE,
         comp_file=comp_file,
         data_loss_mode=args.DATA_LOSS_MODE,
-        contrastive_binding=args.CONTRASTIVE_BINDING
+        contrastive_binding=args.CONTRASTIVE_BINDING,
+        smooth=args.SMOOTHING_INPUT
     )
 
     Es, Ms, Ns, Bs, Ks, Fs, ufs, spins = sim.run_energy_minimization(

{pyloopsage-1.1.6 → pyloopsage-1.1.7}/loopsage/stochastic_simulation.py

@@ -657,7 +657,8 @@ class StochasticSimulation:
             lef_density_file=None,
             comp_file=None,
             data_loss_mode=0,
-            contrastive_binding=True
+            contrastive_binding=True,
+            smooth = False
         ):
             """
             Chromatin stochastic simulation initializer.
@@ -724,7 +725,7 @@ class StochasticSimulation:
  
             # Print basic setup
             log.info(f"Number of beads: {self.N_beads}")
-            self.preprocessing(contrastive_binding)
+            self.preprocessing(contrastive_binding,smooth)
  
             # LEF initialization
             self.N_lef = (
@@ -789,7 +790,7 @@ class StochasticSimulation:
         BWs (np.ndarray): binding weight matrices.
         between_families_penalty (bool): whether to apply penalty for interactions between families.
         '''
-        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/(2*self.N_CTCF), kappa*1e4
+        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))), -2*self.N_beads*b/self.N_CTCF, kappa*1e4
         epi_norm = epi_coeff
         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)
@@ -869,7 +870,7 @@ class StochasticSimulation:
         
         return self.Es, self.Ms, self.Ns, self.Bs, self.Ks, self.Fs, self.ufs, self.epi_states
 
-    def preprocessing(self, contrastive_binding):
+    def preprocessing(self, contrastive_binding, smooth):
         """
         Preprocessing pipeline using updated BEDPE/BED/narrowPeak + BigWig exporters.
  
@@ -892,7 +893,7 @@ class StochasticSimulation:
             viz=True,
             diagonal_interactions=True,
             alpha=1.0,
-            smooth=True,
+            smooth=smooth,
             smooth_sigma=self.N_beads / 100,
             contrastive=contrastive_binding
         )
@@ -1038,8 +1039,7 @@ class StochasticSimulation:
         if not do_compartments: self.epi_states=None
         md = MD_LE(self.Ms,self.Ns,self.epi_states,self.N_beads,self.path,platform,angle_ff_strength,le_distance,le_ff_strength,ev_ff_strength,ev_ff_power,tolerance)
         sim_heat = md.run_pipeline(plots=save_plots,sim_step=sim_step,friction=friction,integrator_step=integrator_step,temperature=temperature,ff_path=ff_path,p_ev=p_ev,init_struct=init_struct,continuous_topoisomerase=continuous_topoisomerase)
-        if self.interaction_file.endswith((".bedpe")):
-            corr_exp_heat(sim_heat,self.interaction_file,self.region,self.chrom,self.N_beads,self.path)
+        corr_exp_heat(sim_heat,self.interaction_file,self.region,self.chrom,self.N_beads,self.path)
 
 def main():
     # Definition of Monte Carlo parameters