py2/3 compatibility

README.rst

@@ -7,16 +7,7 @@
 +-----------------------+-+
 
 
-TADdyn is a Python library that allows to model and explore single or time-series 3C-based data.
-These datasets are constituted by interaction matrices that describe distinct stages of naturally
-occurring or induced cellular process such as the cell trans-differentiation, or reprogramming.
-With TADdyn the user can load at once the raw and normalised interaction binned matrices (Hi-C like matrices)
-at each of the experimental stages, build 4D models, and finally, extract structural properties from the models.
-The 4D models reproduce the expected interaction patterns at the experimental time-points,
-and also describe the structural modifications at intermediate moments (between stages) under the hypothesis
-that the changes occurring between consecutive experimental time-points are smooth. To do this,
-TADdyn is designed as a combination of restraint-based modelling, and steered Langevin dynamics of Physics-based
-chromatin models.
+TADphys.
 
 Documentation
 *************
@@ -25,22 +16,11 @@ Documentation
    | 1 - Download lammps
    | git clone -b stable https://github.com/lammps/lammps.git mylammps
 
-   | 2 - Download the colvar modified version
-   | git clone https://github.com/david-castillo/colvars
-
-   | 3 - Update the user-defined colvars library
-   | ./colvars/update-colvars-code.sh ./mylammps/
-
-   | 4 - Compile colvars library
-   | cd ./mylammps/lib/colvars
-   | make -f Makefile.g++
-
-   | 5 - Install lammps as a shared library
+   | 2 - Install lammps as a shared library
    | cd ../../src/
-   | include "-DLAMMPS_EXCEPTIONS" in the LMP_INC line in src/MAKE/Makefile.serial
-   | make yes-user-colvars
+   | include "-DLAMMPS_EXCEPTIONS" in the LMP_INC line in src/MAKE/Makefile.mpi
    | make yes-molecule
-   | make serial mode=shlib
+   | make mpi mode=shlib
    | make install-python
 
    | cd ../../
@@ -49,38 +29,35 @@ Documentation
    | conda install -y scipy           # scientific computing in python
    | conda install -y numpy           # scientific computing in python
    | conda install -y matplotlib      # to produce plots
-   | conda install -y jupyter         # this notebook :)
    | conda install -y -c https://conda.anaconda.org/bcbio pysam # to deal with SAM/BAM files
-   | conda install -y -c https://conda.anaconda.org/salilab imp # for 3D modeling
-   | conda install -y -c bioconda mcl # for clustering
 
-**Install TADdyn**
-   | 1 - Download TADdyn from the Github repository
-   | git clone https://github.com/david-castillo/TADbit.git -b TADdyn TADdyn
+**Install TADphys**
+   | 1 - Download TADphys from the Github repository
+   | git clone https://github.com/MarcoDiS/TADphys.git -b TADphys TADphys
 
-   | 2 - Install TADdyn
-   | cd TADdyn
+   | 2 - Install TADphys
+   | cd TADphys
    | python setup.py install
    | cd ..
 
 **Try TADdyn**
-   | cd test/Sox2
-   | python test_TADdyn_on_Sox2.py
+   | cd test/
+   | python test_TADphys.py
 
 Citation
 ********
-Please, cite this article if you use TADdyn.
+Please, cite this article if you use TADphys.
 
 Marco Di Stefano, Ralph Stadhouders, Irene Farabella, David Castillo, François Serra, Thomas Graf, Marc A. Marti-Renom.
 **Dynamic simulations of transcriptional control during cell reprogramming reveal spatial chromatin caging.**
 *bioRxiv* 642009; `doi: https://doi.org/10.1101/642009`_
 
-Methods implemented in TADdyn
+Methods implemented in TADphys
 -----------------------------
-In the actual implementation, TADdyn relies on TADbit for the preparation of the 3C-based datasets from mapping to normalization,
+In the actual implementation, TADphys relies on TADbit for the models' analysis
 and on LAMMPS [Plimpton]_ for the implementation of the simulations.
 
 Bibliography
 ************
 
-.. [Plimpton] Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular Dynamics. J Comp Phys 117, 1-19 (1995) and Fiorin, G., Klein, M.L. & Hénin, J. Using collective variables to drive molecular dynamics simulations. Molecular Physics 111, 3345-3362 (2013).
+.. [Plimpton] Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular Dynamics. J Comp Phys 117, 1-19 (1995) and Fiorin, G., Klein, M.L. & Hénin, J. Using collective variables to drive molecular dynamics simulations. Molecular Physics 111, 3345-3362 (2013).

TADphys.egg-info/PKG-INFO

@@ -0,0 +1,73 @@
+Metadata-Version: 1.0
+Name: TADphys
+Version: 0.1
+Summary: Tadphys is a Python library that allows to model and explore single or time-series 3C-based data.
+Home-page: UNKNOWN
+Author: Marco Di Stefano
+Author-email: marco.di.distefano.1985@gmail.com
+License: GPLv3
+Description: 
+
+        +-----------------------+-+
+        |                       | |
+        | Current version: pipeline_v0.2.722  |
+        |                       | |
+        +-----------------------+-+
+
+
+        TADphys.
+
+        Documentation
+        *************
+
+        **Install LAMMPS as a shared library**
+           | 1 - Download lammps
+           | git clone -b stable https://github.com/lammps/lammps.git mylammps
+
+           | 2 - Install lammps as a shared library
+           | cd ../../src/
+           | include "-DLAMMPS_EXCEPTIONS" in the LMP_INC line in src/MAKE/Makefile.mpi
+           | make yes-molecule
+           | make mpi mode=shlib
+           | make install-python
+
+           | cd ../../
+
+        **Install packages**
+           | conda install -y scipy           # scientific computing in python
+           | conda install -y numpy           # scientific computing in python
+           | conda install -y matplotlib      # to produce plots
+           | conda install -y -c https://conda.anaconda.org/bcbio pysam # to deal with SAM/BAM files
+
+        **Install TADphys**
+           | 1 - Download TADphys from the Github repository
+           | git clone https://github.com/MarcoDiS/TADphys.git -b TADphys TADphys
+
+           | 2 - Install TADphys
+           | cd TADphys
+           | python setup.py install
+           | cd ..
+
+        **Try TADdyn**
+           | cd test/
+           | python test_TADphys.py
+
+        Citation
+        ********
+        Please, cite this article if you use TADphys.
+
+        Marco Di Stefano, Ralph Stadhouders, Irene Farabella, David Castillo, François Serra, Thomas Graf, Marc A. Marti-Renom.
+        **Dynamic simulations of transcriptional control during cell reprogramming reveal spatial chromatin caging.**
+        *bioRxiv* 642009; `doi: https://doi.org/10.1101/642009`_
+
+        Methods implemented in TADphys
+        -----------------------------
+        In the actual implementation, TADphys relies on TADbit for the models' analysis
+        and on LAMMPS [Plimpton]_ for the implementation of the simulations.
+
+        Bibliography
+        ************
+
+        .. [Plimpton] Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular Dynamics. J Comp Phys 117, 1-19 (1995) and Fiorin, G., Klein, M.L. & Hénin, J. Using collective variables to drive molecular dynamics simulations. Molecular Physics 111, 3345-3362 (2013).
+
+Platform: OS Independent

TADphys.egg-info/SOURCES.txt

@@ -0,0 +1,29 @@
+README.rst
+setup.py
+TADphys.egg-info/PKG-INFO
+TADphys.egg-info/SOURCES.txt
+TADphys.egg-info/dependency_links.txt
+TADphys.egg-info/top_level.txt
+src/3d-lib/squared_distance_matrix_calculation_py.c
+tadphys/Chromosome_region.py
+tadphys/__init__.py
+tadphys/_version.py
+tadphys/chromosome.py
+tadphys/experiment.py
+tadphys/hic_data.py
+tadphys/modelling/HIC_CONFIG.py
+tadphys/modelling/LAMMPS_CONFIG.py
+tadphys/modelling/__init__.py
+tadphys/modelling/impoptimizer.py
+tadphys/modelling/lammps_modelling.py
+tadphys/modelling/lammpsmodel.py
+tadphys/modelling/restraints.py
+tadphys/modelling/structuralmodel.py
+tadphys/utils/__init__.py
+tadphys/utils/extraviews.py
+tadphys/utils/hic_filtering.py
+tadphys/utils/hic_parser.py
+tadphys/utils/maths.py
+tadphys/utils/modelAnalysis.py
+tadphys/utils/tadmaths.py
+test/test_TADdyn_on_Sox2.py

TADphys.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

TADphys.egg-info/top_level.txt

@@ -0,0 +1 @@
+tadphys

taddyn/__init__.py → build/lib.linux-x86_64-3.6/tadphys/__init__.py

@@ -3,7 +3,7 @@
 from os import environ
 from subprocess import Popen, PIPE, check_call, CalledProcessError
 
-from taddyn._version import __version__
+from tadphys._version import __version__
 
 # ## Check if we have X display http://stackoverflow.com/questions/8257385/automatic-detection-of-display-availability-with-matplotlib
 # if not "DISPLAY" in environ:
@@ -19,11 +19,11 @@
 
 def get_dependencies_version(dico=False):
     """
-    Check versions of TADdyn and all dependencies, as well and retrieves system
+    Check versions of TADphys and all dependencies, as well and retrieves system
     info. May be used to ensure reproducibility.
     :returns: string with description of versions installed
     """
-    versions = {'  TADdyn': __version__ + '\n\n'}
+    versions = {'  TADphys': __version__ + '\n\n'}
 
     try:
         import scipy
@@ -62,11 +62,11 @@ def get_dependencies_version(dico=False):
                           sorted(versions.keys())])
 
 
-from taddyn.chromosome                 import Chromosome
-from taddyn.experiment                 import Experiment, load_experiment_from_reads
-from taddyn.chromosome                 import load_chromosome
+from tadphys.chromosome                 import Chromosome
+from tadphys.experiment                 import Experiment, load_experiment_from_reads
+from tadphys.chromosome                 import load_chromosome
 # from taddyn.modelling.structuralmodels import StructuralModels
 # from taddyn.modelling.structuralmodels import load_structuralmodels
 # from taddyn.utils.hic_parser         import load_hic_data_from_reads
 # from taddyn.utils.hic_parser         import load_hic_data_from_bam
-from taddyn.utils.hic_parser         import read_matrix
+from tadphys.utils.hic_parser         import read_matrix

taddyn/chromosome.py → build/lib.linux-x86_64-3.6/tadphys/chromosome.py

@@ -5,14 +5,14 @@
 
 from string                            import ascii_lowercase as letters
 from copy                              import deepcopy as copy
-from cPickle                           import load, dump
+from pickle                            import load, dump
 from random                            import random
 from math                              import sqrt
 from sys                               import stderr
 from os.path                           import exists
-import taddyn
-from taddyn.experiment               import Experiment
-# from taddyn.alignment                import Alignment, randomization_test
+import tadphys
+from tadphys.experiment               import Experiment
+# from tadphys.alignment                import Alignment, randomization_test
 
 try:
     import matplotlib.pyplot as plt
@@ -276,7 +276,7 @@ def get_experiment(self, name):
         This can also be done directly with Chromosome.experiments[name].
 
         :param name: name of the experiment to select
-        :returns: :class:`taddyn.Experiment`
+        :returns: :class:`tadphys.Experiment`
         """
         for exp in self.experiments:
             if exp.name == name:
@@ -379,9 +379,9 @@ def save_chromosome(self, out_f, fast=True, divide=True, force=False):
     #        simply shuffled
     #     :param 1000 rnd_num: number of randomizations to do
     #     :param reciprocal method: if global, Needleman-Wunsch is used to align
-    #         (see :func:`taddyn.boundary_aligner.globally.needleman_wunsch`);
+    #         (see :func:`tadphys.boundary_aligner.globally.needleman_wunsch`);
     #         if reciprocal, a method based on reciprocal closest boundaries is
-    #         used (see :func:`taddyn.boundary_aligner.reciprocally.reciprocal`)
+    #         used (see :func:`tadphys.boundary_aligner.reciprocally.reciprocal`)
 
     #     :returns: an alignment object or, if the randomizattion was invoked,
     #        an alignment object, and a list of statistics that are, the alignment
@@ -485,7 +485,7 @@ def add_experiment(self, name, resolution=None, tad_def=None, hic_data=None,
     #              verbose=True, max_tad_size="max", heuristic=True,
     #              batch_mode=False, **kwargs):
     #     """
-    #     Call the :func:`taddyn.tadbit.tadbit` function to calculate the
+    #     Call the :func:`tadphys.tadbit.tadbit` function to calculate the
     #     position of Topologically Associated Domain boundaries
 
     #     :param experiment: A square matrix of interaction counts of Hi-C
@@ -639,7 +639,7 @@ def __update_size(self, xpr):
     #     :param True normalized: show the normalized data (weights might have
     #        been calculated previously). *Note: white rows/columns may appear in
     #        the matrix displayed; these rows correspond to filtered rows (see*
-    #        :func:`taddyn.utils.hic_filtering.hic_filtering_for_modelling` *)*
+    #        :func:`tadphys.utils.hic_filtering.hic_filtering_for_modelling` *)*
     #     :param True relative: color scale is relative to the whole matrix of
     #        data, not only to the region displayed
     #     :param True decorate: draws color bar, title and axes labels
@@ -903,14 +903,14 @@ def __update_size(self, xpr):
 class ExperimentList(list):
     """
     Inherited from python built in :py:func:`list`, modified for TADbit
-    :class:`taddyn.Experiment`.
+    :class:`tadphys.Experiment`.
 
     Mainly, `getitem`, `setitem`, and `append` were modified in order to
     be able to search for experiments by index or by name, and to add
     experiments simply using Chromosome.experiments.append(Experiment).
 
     The whole ExperimentList object is linked to a Chromosome instance
-    (:class:`taddyn.Chromosome`).
+    (:class:`tadphys.Chromosome`).
 
     """
     def __init__(self, thing, crm):
@@ -971,12 +971,12 @@ def append(self, exp):
 
 class AlignmentDict(dict):
     """
-    :py:func:`dict` of :class:`taddyn.Alignment`
+    :py:func:`dict` of :class:`tadphys.Alignment`
 
     Modified getitem, setitem, and append in order to be able to search
     alignments by index or by name.
 
-    linked to a :class:`taddyn.Chromosome`
+    linked to a :class:`tadphys.Chromosome`
     """
 
     def __getitem__(self, nam):