pyCoReGraph 0.0.1a1__py3-none-any.whl

coregraph/utils/decorators.py

@@ -0,0 +1,39 @@
+## DECORATORS ##
+
+from functools import wraps
+
+
+def requires_cors(func):
+    @wraps(func)
+    def wrapper(coregraph, *args, **kwargs):
+        if coregraph.cors.window is None:
+            raise RuntimeError(
+                "Correlations have not been calculated yet. "
+                "Run `calculate_all_cors()` first."
+            )
+        return func(coregraph, *args, **kwargs)
+    return wrapper
+
+
+def requires_bins(func):
+    @wraps(func)
+    def wrapper(coregraph, *args, **kwargs):
+        if coregraph.graphics.n_bins is None:
+            raise RuntimeError(
+                "Bins have not been discretized yet. "
+                "Run `calculate_bins()` first."
+            )
+        return func(coregraph, *args, **kwargs)
+    return wrapper
+
+
+def requires_FDR(func):
+    @wraps(func)
+    def wrapper(coregraph, *args, **kwargs):
+        if coregraph.cors.FDR is None:
+            raise RuntimeError(
+                "FDR has not been computed yet. "
+                "Run `calculate_FDR()` first."
+            )
+        return func(coregraph, *args, **kwargs)
+    return wrapper

coregraph/utils/formatting.py

@@ -0,0 +1,16 @@
+## FORMATTING ##
+
+import numpy as np
+
+
+def _set_numerical_format(dtype: str):
+        '''Assign correct numerical parametrs depending on dtype sepcified from user'''
+        if isinstance(dtype, str):
+            if dtype.lower() == 'float':
+                return [np.float64, np.array([1,15])]
+            elif dtype.lower() == 'int':
+                return [np.int64, np.array([1000,0])]
+        else:
+            raise ValueError("dtype must be 'int' or 'float'")
+            
+            

coregraph/utils/validation.py

@@ -0,0 +1,25 @@
+## VALIDATION ##
+
+import math
+
+
+def _solve_step(step, n_steps, window, n_cells):
+    if (step == None) and (n_steps == None):
+        return 1, n_cells-window+1
+    if (step != None) and (n_steps != None):
+        raise ValueError("Specify either 'step' or 'n_steps, not both.")
+    if (step != None):
+        if (step >= (n_cells - window)):
+            raise ValueError("'step' is too high for provided window")
+        else:
+            n_steps = (n_cells - window) // step + 1
+            return step, n_steps
+    if n_steps >= (n_cells - window):
+        raise ValueError("'n_steps' is too high for provided window")
+    else:
+        step = math.ceil((n_cells - window) / n_steps)
+        return step, n_steps
+
+def _solve_total_dim3(step, window, n_cells):
+    max_dim = (n_cells - window) // step + 1
+    return max_dim * (max_dim + 1) //2

pycoregraph-0.0.1a1.dist-info/METADATA

@@ -0,0 +1,65 @@
+Metadata-Version: 2.4
+Name: pyCoReGraph
+Version: 0.0.1a1
+Summary: CoReGraph : Correlation-based dynamic gene Regulatory Graphs
+Author-email: Joseph Léger <josephleger@outlook.fr>
+License: MIT
+Project-URL: Homepage, https://github.com/JosephLeger/CoReGraph
+Project-URL: Repository, https://github.com/JosephLeger/CoReGraph
+Project-URL: Issues, https://github.com/JosephLeger/CoReGraph/issues
+Keywords: bioinformatics,single-cell,gene-regulatory-network,pseudotime,correlation,network-analysis,visualization
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: networkx>=3.0
+Requires-Dist: scipy>=1.10
+Requires-Dist: tqdm>=4.65
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Requires-Dist: black>=24.0; extra == "dev"
+Requires-Dist: ipykernel>=6.0; extra == "dev"
+Provides-Extra: notebook
+Requires-Dist: jupyter>=1.0; extra == "notebook"
+Requires-Dist: ipython>=8.0; extra == "notebook"
+Provides-Extra: all
+Requires-Dist: pytest>=8.0; extra == "all"
+Requires-Dist: build>=1.0; extra == "all"
+Requires-Dist: twine>=5.0; extra == "all"
+Requires-Dist: ruff>=0.4; extra == "all"
+Requires-Dist: black>=24.0; extra == "all"
+Requires-Dist: ipykernel>=6.0; extra == "all"
+Requires-Dist: jupyter>=1.0; extra == "all"
+Requires-Dist: ipython>=8.0; extra == "all"
+Dynamic: license-file
+
+# CoReGraph : **Co**rrelation-based dynamic gene **Re**gulatory **Graph**s
+
+A Python package for dynamic lagged gene correlation analysis along pseudotime trajectories.
+
+## Requirments
+
+```bash
+python >= 3.10
+```
+
+## Installation
+
+```bash
+pip install coregraph
+```

pycoregraph-0.0.1a1.dist-info/RECORD

@@ -0,0 +1,26 @@
+coregraph/__init__.py,sha256=SzuGoHBO0vM0kkQjO2dkcegJXFWWzJ3b-S2uFpttG7M,1070
+coregraph/analysis/__init__.py,sha256=o0W0KYqTIZg8GD2EWr6ZpK8twqq3g8N2ww7u2cyYt7s,787
+coregraph/analysis/bins.py,sha256=bQEGC2xYy1cKdDxfsLFae6Z6zlJM5uusLsRDmMk-Fb0,790
+coregraph/analysis/correlations.py,sha256=7n4aZ0LbUXunqtTYUdEpGJ1EfL62whwMcJ53jamFJYE,4506
+coregraph/analysis/fdr.py,sha256=RmI2jqlDfZrTyeK2k2IiOiAIIZGHzmFJ9XilaIdeFZU,3820
+coregraph/analysis/queries.py,sha256=mjzy6HXp7Dqe_dz19eRW609O6WLLZbVVObRIC-fJMUI,3641
+coregraph/analysis/subset.py,sha256=QXIX5EldiIPQrz_EHN3SYT4SrrFIwSiiGzSCtzkuWks,2313
+coregraph/graphics/__init__.py,sha256=HDGSQXTEkdzJrXv7YuA3VJaPxUW4Cbis1bvi3n_d17g,436
+coregraph/graphics/animations.py,sha256=dyB9yzmIaQFxoJrV_RgC1ENRIEOsCSJ7mLuu-JTOcB4,2180
+coregraph/graphics/colors.py,sha256=H79l9Wy1OBLc_zw2j1lxJ8LWEeNOxMbNhEyyI-MOGb0,474
+coregraph/graphics/network.py,sha256=g2B0vonB-TqLqIpHPa3Lqi4iubbrVbl1Mg7FPVWzjPI,6083
+coregraph/graphics/plots.py,sha256=eTCrSTDu1ImIKzkMd1j3NrKsNtXPMnbEHK3vsGgb-mk,3111
+coregraph/models/__init__.py,sha256=x9tzA6LJ7Iz8MP-xZsmBrSNLcykHcyI-HXVVzqHghz4,246
+coregraph/models/coregraph.py,sha256=dSsVf-kEls-RaXBsN8FJ977qFCpOMUTPVRGdq1dyo-M,8817
+coregraph/models/cors.py,sha256=J0CYYbqPCoua6TF_IVJFXZBjfKEHNE2DUg01xtbm5Wo,1983
+coregraph/models/graphics.py,sha256=USdExX5w-eBIu67Y48WPTB4bL1cYl8PgCq0pKMSRq0U,844
+coregraph/models/stargraph.py,sha256=W69BgIwbvzOFAhtaxCemy7hFUOLtXp4jZ5rlIhdxzIs,1258
+coregraph/utils/__init__.py,sha256=V6q1VN3P--1vJV2z_abiyOI4fUfOY4raE3fkVb2Mu3k,380
+coregraph/utils/decorators.py,sha256=p-M9POAqeEQYrGs-EDj-jz0mQPsXK1BaC8ayvnWRdSs,1129
+coregraph/utils/formatting.py,sha256=WA1E0N9w7QxR_elh0dVTIBuIBqpss7ERUE0xoIoG9WE,508
+coregraph/utils/validation.py,sha256=h3S-oXeulsbbh4HPJS33hA1eX_SBkdCeS-cLbx7MNH8,870
+pycoregraph-0.0.1a1.dist-info/licenses/LICENSE,sha256=pJCrZwHnShCXTiMCrr9x9K0YntP8duL21c-WhUpAVQA,1068
+pycoregraph-0.0.1a1.dist-info/METADATA,sha256=4lCV8s50kF4r84HBRNQZrGk6--vVX9_K02T-I03RxA8,2384
+pycoregraph-0.0.1a1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+pycoregraph-0.0.1a1.dist-info/top_level.txt,sha256=f5n-iVpzU4mX6tmszRB3ZbEs-q3iPaaITA1nz05BR3A,10
+pycoregraph-0.0.1a1.dist-info/RECORD,,

pycoregraph-0.0.1a1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

pycoregraph-0.0.1a1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 JosephLeger
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pycoregraph-0.0.1a1.dist-info/top_level.txt

@@ -0,0 +1 @@
+coregraph