pyLoopSage 0.0.6__tar.gz → 0.1.0__tar.gz

{pyloopsage-0.0.6 → pyloopsage-0.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 0.0.6
+Version: 0.1.0
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -29,6 +29,7 @@ Requires-Dist: OpenMM
 Requires-Dist: OpenMM-cuda
 Requires-Dist: statsmodels
 Requires-Dist: imageio
+Requires-Dist: imageio[ffmpeg]
 Requires-Dist: pillow
 
 # pyLoopSage
@@ -50,14 +51,14 @@ Please cite the method paper in case that you would like to use this model for y
 
 ## The model
 
-We have a polymer chain with $$N_{\text{beads}}$$ number of monomers. In general we can scale by deault the granularity of the simulation so as to give reasonable results. Therefore if we have a `region` counted in genomic coordinates, we can assume that `N_beads=(region[1]-region[0])//2000`.
+We have a polymer chain with $N_{\text{beads}}$ number of monomers. In general we can scale by deault the granularity of the simulation so as to give reasonable results. Therefore if we have a `region` counted in genomic coordinates, we can assume that `N_beads=(region[1]-region[0])//2000`.
 
 Let's assume that each cohesin $i$ can be represented of two coordinates $(m_{i},n_{i})$ we allow three moves in our simulation:
 
 * Slide both locations randomly (as 1D random walk) or
 * Rebind somewhere else.
 
-In general a good working assumption is that the number of cohesins (or loop extrusion factors LEFs) is $$N_{\text{lef}}=2N_{\text{CTCF}}$$.
+In general a good working assumption is that the number of cohesins (or loop extrusion factors LEFs) is $N_{\text{lef}}=2N_{\text{CTCF}}$.
 
 The main idea of the algorithm is to ensemble loop extrusion from a Boltzmann probability distribution, with Hamiltonian,
 
@@ -70,7 +71,7 @@ These $L(\cdot), R(\cdot)$ functions are two functions that define the binding p
 
 $$c_{\text{fold}}=-\dfrac{N_{\text{beads}}f}{N_{\text{lef}}\log(N_{\text{beads}}/N_{\text{lef}})},\quad c_{\text{bind}}=-\dfrac{N_{\text{beads}}b}{\sum_i \left(L(m_i)+R(n_i)\right)},\quad c_{\text{cross}}=\kappa \times 10^4.$$
 
-The parameters are defined in such a way that when $$f=b=\kappa=1$$, the three terms of the stochastic energy are balanced. 
+The parameters are defined in such a way that when $f=b=\kappa=1$, the three terms of the stochastic energy are balanced. 
 
 And the energy difference can be expressed as the energy difference of each term,
 
@@ -95,7 +96,7 @@ The main script is `LoopSage.py`. The implementation of the code is very easy an
 
 ```python
 # Definition of Monte Carlo parameters
-import Loopsage.stochastic_simulation as lps
+import loopsage.stochastic_simulation as lps
 
 N_steps, MC_step, burnin, T, T_min = int(4e4), int(5e2), 1000, 2.5, 1.0
 mode = 'Metropolis'

{pyloopsage-0.0.6 → pyloopsage-0.1.0}/README.md

@@ -17,14 +17,14 @@ Please cite the method paper in case that you would like to use this model for y
 
 ## The model
 
-We have a polymer chain with $$N_{\text{beads}}$$ number of monomers. In general we can scale by deault the granularity of the simulation so as to give reasonable results. Therefore if we have a `region` counted in genomic coordinates, we can assume that `N_beads=(region[1]-region[0])//2000`.
+We have a polymer chain with $N_{\text{beads}}$ number of monomers. In general we can scale by deault the granularity of the simulation so as to give reasonable results. Therefore if we have a `region` counted in genomic coordinates, we can assume that `N_beads=(region[1]-region[0])//2000`.
 
 Let's assume that each cohesin $i$ can be represented of two coordinates $(m_{i},n_{i})$ we allow three moves in our simulation:
 
 * Slide both locations randomly (as 1D random walk) or
 * Rebind somewhere else.
 
-In general a good working assumption is that the number of cohesins (or loop extrusion factors LEFs) is $$N_{\text{lef}}=2N_{\text{CTCF}}$$.
+In general a good working assumption is that the number of cohesins (or loop extrusion factors LEFs) is $N_{\text{lef}}=2N_{\text{CTCF}}$.
 
 The main idea of the algorithm is to ensemble loop extrusion from a Boltzmann probability distribution, with Hamiltonian,
 
@@ -37,7 +37,7 @@ These $L(\cdot), R(\cdot)$ functions are two functions that define the binding p
 
 $$c_{\text{fold}}=-\dfrac{N_{\text{beads}}f}{N_{\text{lef}}\log(N_{\text{beads}}/N_{\text{lef}})},\quad c_{\text{bind}}=-\dfrac{N_{\text{beads}}b}{\sum_i \left(L(m_i)+R(n_i)\right)},\quad c_{\text{cross}}=\kappa \times 10^4.$$
 
-The parameters are defined in such a way that when $$f=b=\kappa=1$$, the three terms of the stochastic energy are balanced. 
+The parameters are defined in such a way that when $f=b=\kappa=1$, the three terms of the stochastic energy are balanced. 
 
 And the energy difference can be expressed as the energy difference of each term,
 
@@ -62,7 +62,7 @@ The main script is `LoopSage.py`. The implementation of the code is very easy an
 
 ```python
 # Definition of Monte Carlo parameters
-import Loopsage.stochastic_simulation as lps
+import loopsage.stochastic_simulation as lps
 
 N_steps, MC_step, burnin, T, T_min = int(4e4), int(5e2), 1000, 2.5, 1.0
 mode = 'Metropolis'

{pyloopsage-0.0.6 → pyloopsage-0.1.0}/pyLoopSage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 0.0.6
+Version: 0.1.0
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -29,6 +29,7 @@ Requires-Dist: OpenMM
 Requires-Dist: OpenMM-cuda
 Requires-Dist: statsmodels
 Requires-Dist: imageio
+Requires-Dist: imageio[ffmpeg]
 Requires-Dist: pillow
 
 # pyLoopSage
@@ -50,14 +51,14 @@ Please cite the method paper in case that you would like to use this model for y
 
 ## The model
 
-We have a polymer chain with $$N_{\text{beads}}$$ number of monomers. In general we can scale by deault the granularity of the simulation so as to give reasonable results. Therefore if we have a `region` counted in genomic coordinates, we can assume that `N_beads=(region[1]-region[0])//2000`.
+We have a polymer chain with $N_{\text{beads}}$ number of monomers. In general we can scale by deault the granularity of the simulation so as to give reasonable results. Therefore if we have a `region` counted in genomic coordinates, we can assume that `N_beads=(region[1]-region[0])//2000`.
 
 Let's assume that each cohesin $i$ can be represented of two coordinates $(m_{i},n_{i})$ we allow three moves in our simulation:
 
 * Slide both locations randomly (as 1D random walk) or
 * Rebind somewhere else.
 
-In general a good working assumption is that the number of cohesins (or loop extrusion factors LEFs) is $$N_{\text{lef}}=2N_{\text{CTCF}}$$.
+In general a good working assumption is that the number of cohesins (or loop extrusion factors LEFs) is $N_{\text{lef}}=2N_{\text{CTCF}}$.
 
 The main idea of the algorithm is to ensemble loop extrusion from a Boltzmann probability distribution, with Hamiltonian,
 
@@ -70,7 +71,7 @@ These $L(\cdot), R(\cdot)$ functions are two functions that define the binding p
 
 $$c_{\text{fold}}=-\dfrac{N_{\text{beads}}f}{N_{\text{lef}}\log(N_{\text{beads}}/N_{\text{lef}})},\quad c_{\text{bind}}=-\dfrac{N_{\text{beads}}b}{\sum_i \left(L(m_i)+R(n_i)\right)},\quad c_{\text{cross}}=\kappa \times 10^4.$$
 
-The parameters are defined in such a way that when $$f=b=\kappa=1$$, the three terms of the stochastic energy are balanced. 
+The parameters are defined in such a way that when $f=b=\kappa=1$, the three terms of the stochastic energy are balanced. 
 
 And the energy difference can be expressed as the energy difference of each term,
 
@@ -95,7 +96,7 @@ The main script is `LoopSage.py`. The implementation of the code is very easy an
 
 ```python
 # Definition of Monte Carlo parameters
-import Loopsage.stochastic_simulation as lps
+import loopsage.stochastic_simulation as lps
 
 N_steps, MC_step, burnin, T, T_min = int(4e4), int(5e2), 1000, 2.5, 1.0
 mode = 'Metropolis'

{pyloopsage-0.0.6 → pyloopsage-0.1.0}/pyLoopSage.egg-info/requires.txt

@@ -15,4 +15,5 @@ OpenMM
 OpenMM-cuda
 statsmodels
 imageio
+imageio[ffmpeg]
 pillow

{pyloopsage-0.0.6 → pyloopsage-0.1.0}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='0.0.6',  # Version of the software
+    version='0.1.0',  # 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',
@@ -33,11 +33,12 @@ setup(
         'OpenMM-cuda',
         'statsmodels',
         'imageio',
+        'imageio[ffmpeg]',
         'pillow',
     ],
     entry_points={
         'console_scripts': [
-            'loopsage=LoopSage.run:main',  # MultiMM command points to run.py's main function
+            'loopsage=LoopSage.run:main',  # loopsage command points to run.py's main function
         ],
     },
     classifiers=[