pyLoopSage 1.1.0__tar.gz → 1.1.1__tar.gz

{pyloopsage-1.1.0/pyLoopSage.egg-info → pyloopsage-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLoopSage
-Version: 1.1.0
+Version: 1.1.1
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -313,7 +313,7 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 | 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                 |
-| BW_STRENGTHS          | List of strengths corresponding to each .bw file.                                                              | list       | None                  |
+| BW_STRENGTHS          | List of strengths of the energy (floats) corresponding to each BW file. This equivalent to the `r` parameter in the LoopSage paper.                                                              | list       | None                  |
 
 #### Molecular Dynamics Simulation
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |

{pyloopsage-1.1.0 → pyloopsage-1.1.1}/README.md

@@ -267,7 +267,7 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 | 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                 |
-| BW_STRENGTHS          | List of strengths corresponding to each .bw file.                                                              | list       | None                  |
+| BW_STRENGTHS          | List of strengths of the energy (floats) corresponding to each BW file. This equivalent to the `r` parameter in the LoopSage paper.                                                              | list       | None                  |
 
 #### Molecular Dynamics Simulation
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |

{pyloopsage-1.1.0 → pyloopsage-1.1.1}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.1.0"
+__version__ = "1.1.1"

{pyloopsage-1.1.0 → pyloopsage-1.1.1}/loopsage/stochastic_simulation.py

@@ -154,12 +154,12 @@ def slide(m_old, n_old, ms, ns, N_beads, rw=True, drift=True):
     choices = np.array([-1, 1], dtype=np.int64)
     r1 = np.random.choice(choices) if rw else -1
     r2 = np.random.choice(choices) if rw else 1
-    m_new = m_old + r1 if m_old + r1>=0 else 0
-    if np.any(ns==m_new) and drift and m_old-r1<n_old-1: 
-        m_new =  m_old - r1 if m_old + r1>=0 else 0
-    n_new = n_old + r2 if n_old + r2<N_beads else N_beads-1
-    if np.any(ms==n_new) and drift and n_old-r2>m_old+1: 
-        n_new =  n_old - r2 if n_old + r2<N_beads else N_beads-1
+    m_new = max(m_old + r1, 0)
+    if np.any(ns == m_new) and drift and m_old - r1 < n_old - 1: 
+        m_new = max(m_old - r1, 0)
+    n_new = min(n_old + r2, N_beads - 1)
+    if np.any(ms == n_new) and drift and n_old - r2 > m_old + 1: 
+        n_new = min(n_old - r2, N_beads - 1)
     return int(m_new), int(n_new)
 
 @njit

{pyloopsage-1.1.0 → pyloopsage-1.1.1/pyLoopSage.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLoopSage
-Version: 1.1.0
+Version: 1.1.1
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -313,7 +313,7 @@ An example, illustrated with Chimera software, simulated trajectory of structure
 | 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                 |
-| BW_STRENGTHS          | List of strengths corresponding to each .bw file.                                                              | list       | None                  |
+| BW_STRENGTHS          | List of strengths of the energy (floats) corresponding to each BW file. This equivalent to the `r` parameter in the LoopSage paper.                                                              | list       | None                  |
 
 #### Molecular Dynamics Simulation
 | Argument Name          | Description                                                                                                     | Type        | Default Value       |

{pyloopsage-1.1.0 → pyloopsage-1.1.1}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='1.1.0',  # Version of the software
+    version='1.1.1',  # 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',