maradoner 0.14.2__tar.gz → 0.15.0__tar.gz

{maradoner-0.14.2 → maradoner-0.15.0}/PKG-INFO

@@ -1,17 +1,16 @@
 Metadata-Version: 2.1
 Name: maradoner
-Version: 0.14.2
+Version: 0.15.0
 Summary: Variance-adjusted estimation of motif activities.
-Home-page: https://github.com/autosome-ru/nemara
+Home-page: https://github.com/autosome-ru/maradoner
 Author: Georgy Meshcheryakov
 Author-email: iam@georgy.top
-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: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.9
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 Requires-Dist: pip>=24.0
 Requires-Dist: typer>=0.13
@@ -27,6 +26,7 @@ Requires-Dist: dill>=0.3.9
 Requires-Dist: rich>=12.6.0
 Requires-Dist: tqdm>=4.0
 Requires-Dist: scikit-learn>=1.6
+Requires-Dist: tables>=3.10
 
 
 **MARADONER**

{maradoner-0.14.2 → maradoner-0.15.0}/maradoner/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-__version__ = '0.14.2'
+__version__ = '0.15.0'
 import importlib
 
 
@@ -17,7 +17,8 @@ __min_reqs__ = [
             'dill>=0.3.9',
             'rich>=12.6.0',
             'tqdm>=4.0',
-            'scikit-learn>=1.6'
+            'scikit-learn>=1.6',
+            'tables>=3.10'
            ]
 
 def versiontuple(v):

{maradoner-0.14.2 → maradoner-0.15.0}/maradoner/grn.py

@@ -60,6 +60,8 @@ def estimate_promoter_variance(project_name: str, prior_top=0.90):
     B_hat = B ** 2 * fit.motif_variance.motif
     B_hat = B_hat.sum(axis=1)
     var = list()
+    jax.config.update('jax_enable_x64', True)
+    jax.config.update('jax_platform_name', 'cpu') 
     for inds, prior_mean, nu in tqdm(list(zip(group_inds, prior_means, fit.motif_variance.group))):
         Yt = Y[:, inds].sum(axis=1)
         s = len(inds)
@@ -120,7 +122,7 @@ def bayesian_fdr_control(p0, alpha=0.05):
     return discoveries, threshold
 
 def grn(project_name: str,  output: str, use_hdf=False, save_stat=True,
-        fdr_alpha=0.05, prior_h1=1/100):
+        fdr_alpha=0.05, prior_h1=1/100, include_mean: bool = True):
     data = read_init(project_name)
     fmt = data.fmt
     with openers[fmt](f'{project_name}.fit.{fmt}', 'rb') as f:
@@ -176,13 +178,16 @@ def grn(project_name: str,  output: str, use_hdf=False, save_stat=True,
         os.makedirs(folder_stat, exist_ok=True)
     os.makedirs(folder_belief, exist_ok=True)
     for sigma, nu, name, inds in zip(promvar.T[..., None], nus,  group_names, group_inds):
-        # if name != 'anconeus':
-        #     continue
         print(name)
         var = (B_hat * nu + sigma)
-        Y_ = Y[:, inds][..., None, :] + BM
-        # theta = U[:, inds][..., None, :] + BM
-        theta = B[..., None] * U[:, inds] + BM
+        
+        Y_ = Y[:, inds][..., None, :] 
+        theta = B[..., None] * U[:, inds] 
+        if include_mean:
+            Y_ = Y_ + BM
+            theta = theta + BM
+            
+        
         loglr = 2 * B * (Y_ * theta).sum(axis=-1) - B_pow * (theta ** 2).sum(axis=-1)
         del Y_
         del theta

{maradoner-0.14.2 → maradoner-0.15.0}/maradoner/main.py

@@ -314,18 +314,19 @@ def _select_motifs(name: str = Argument(..., help='Project name'),
 
 __grn_doc = 'Tests each promoter against each motif per each group. Some people call it GRN.'
 @app.command('grn',
-             help=__select_motif_doc)
+             help=__grn_doc)
 def _grn(name: str = Argument(..., help='Project name'),
          folder: Path = Argument(..., help='Output folder where results will be stored. In total, expect number_of_groups tables of size'
                                            ' comparable to the expression file size.'),
          hdf: bool = Option(True, help='Use HDF format instead of tar.gz files. Typically eats much less space'),
          stat: bool = Option(True, help='Save statistics alongside probabilities.'),
-         prior_h1: float = Option(1/10, help='Prior belief on the expected fraction of motifs active per promoter.')):
+         prior_h1: float = Option(1/10, help='Prior belief on the expected fraction of motifs active per promoter.'),
+         means: bool = Option(True, help='Include motif-specific means in both H_0 and H_1 models, otherwise only activities deviations are being tested.')):
     t0 = time()
     p = Progress(SpinnerColumn(speed=0.5), TextColumn("[progress.description]{task.description}"), transient=True)
     p.add_task(description="Building GRN...", total=None)
     p.start()
-    grn(name, output=folder, use_hdf=hdf, save_stat=stat, prior_h1=prior_h1)
+    grn(name, output=folder, use_hdf=hdf, save_stat=stat, prior_h1=prior_h1, include_mean=means)
     p.stop()
     dt = time() - t0
     rprint(f'[green][bold]✔️[/bold] Done![/green]\t time: {dt:.2f} s.')

{maradoner-0.14.2 → maradoner-0.15.0}/maradoner.egg-info/PKG-INFO

@@ -1,17 +1,16 @@
 Metadata-Version: 2.1
 Name: maradoner
-Version: 0.14.2
+Version: 0.15.0
 Summary: Variance-adjusted estimation of motif activities.
-Home-page: https://github.com/autosome-ru/nemara
+Home-page: https://github.com/autosome-ru/maradoner
 Author: Georgy Meshcheryakov
 Author-email: iam@georgy.top
-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: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.9
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 Requires-Dist: pip>=24.0
 Requires-Dist: typer>=0.13
@@ -27,6 +26,7 @@ Requires-Dist: dill>=0.3.9
 Requires-Dist: rich>=12.6.0
 Requires-Dist: tqdm>=4.0
 Requires-Dist: scikit-learn>=1.6
+Requires-Dist: tables>=3.10
 
 
 **MARADONER**

{maradoner-0.14.2 → maradoner-0.15.0}/maradoner.egg-info/requires.txt

@@ -12,3 +12,4 @@ dill>=0.3.9
 rich>=12.6.0
 tqdm>=4.0
 scikit-learn>=1.6
+tables>=3.10

{maradoner-0.14.2 → maradoner-0.15.0}/setup.py

@@ -23,13 +23,12 @@ setup(
     author='Georgy Meshcheryakov',
     author_email='iam@georgy.top',
     install_requires=__min_reqs__,
-    python_requires='>=3.9',
-    url="https://github.com/autosome-ru/nemara",
+    python_requires='>=3.11',
+    url="https://github.com/autosome-ru/maradoner",
     classifiers=[
-	      "Programming Language :: Python :: 3.9",
-	      "Programming Language :: Python :: 3.10",
 	      "Programming Language :: Python :: 3.11",
 	      "Programming Language :: Python :: 3.12",
+	      "Programming Language :: Python :: 3.13",
 	      "Topic :: Scientific/Engineering",
               "Operating System :: OS Independent"]