SigProfilerAssignment 0.1.8__tar.gz → 0.2.0__tar.gz

{SigProfilerAssignment-0.1.8/SigProfilerAssignment.egg-info → sigprofilerassignment-0.2.0}/PKG-INFO

@@ -1,14 +1,35 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: SigProfilerAssignment
-Version: 0.1.8
+Version: 0.2.0
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
 Author-email: rvangara@health.ucsd.edu
 License: UCSD
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
-Provides-Extra: tests
 License-File: LICENSE.txt
+Requires-Dist: scipy>=1.13
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
+Requires-Dist: sigProfilerPlotting>=1.4.0
+Requires-Dist: reportlab>=3.5.42
+Requires-Dist: pypdf>=5.0.0
+Requires-Dist: alive_progress>=2.4.1
+Requires-Dist: PyMuPDF>=1.21.0
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/mz79v/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)

{SigProfilerAssignment-0.1.8 → sigprofilerassignment-0.2.0}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py

@@ -279,18 +279,18 @@ def calculate_similarities(denovo, denovo_name, est_denovo):
 
     # If matrix is 1536 context, then collapse it to 96 format
     if denovo.shape[0] == 1536:
-        index = denovo.iloc[:, 0]
-        denovo_tmp = pd.DataFrame(denovo, index=index)
-        denovo_tmp = denovo.groupby(denovo_tmp.index.str[1:8]).sum()
-        denovo = pd.DataFrame(denovo_tmp)
-        denovo = denovo.reset_index()
-    elif denovo.shape[0] == 288:
-        index = denovo.iloc[:, 0]
-        denovo_tmp = pd.DataFrame(denovo, index=index)
-        denovo_tmp = denovo.groupby(denovo_tmp.index.str[2:9]).sum()
-        denovo = pd.DataFrame(denovo_tmp)
-        denovo = denovo.reset_index()
+        denovo["IndexKey"] = denovo.iloc[:, 0].astype(str)
+        denovo["GroupKey"] = denovo["IndexKey"].str[1:8]
+        denovo_grouped = denovo.groupby("GroupKey", as_index=False).sum(numeric_only=True)
+        denovo_grouped.rename(columns={"GroupKey": "MutationType"}, inplace=True)
+        denovo = denovo_grouped.reset_index(drop=True)
 
+    elif denovo.shape[0] == 288:
+        denovo["MutationType"] = denovo["MutationType"].astype(str)  # Ensure strings
+        denovo["GroupKey"] = denovo["MutationType"].str[2:9]  # Extract substring for grouping
+        denovo_grouped = denovo.groupby("GroupKey", as_index=False).sum(numeric_only=True)
+        denovo_grouped.rename(columns={"GroupKey": "MutationType"}, inplace=True)
+        denovo = denovo_grouped.reset_index(drop=True) # updated pandas 2.0.0
     sample_names = [denovo_name]
 
     if sample_names is False:

{SigProfilerAssignment-0.1.8 → sigprofilerassignment-0.2.0}/SigProfilerAssignment/decompose_subroutines.py

@@ -23,7 +23,7 @@ import string
 import pypdf
 import scipy
 
-from pypdf import PdfMerger
+from pypdf import PdfWriter, PdfReader
 import SigProfilerAssignment as spa
 from SigProfilerAssignment import single_sample as ss
 from scipy.spatial.distance import correlation as cor
@@ -410,7 +410,7 @@ def signature_decomposition(
     )
     # lognote.write("\n********** Starting Signature Decomposition **********\n\n")
     activity_percentages = []
-    merger = PdfMerger()
+    merger = PdfWriter()
 
     for i, j in zip(range(signatures.shape[1]), denovo_signature_names):
         # Only for context SBS96
@@ -606,7 +606,12 @@ def signature_decomposition(
                 exome=exome,
                 volume=volume,
             )
-            merger.append(byte_plot)
+
+            byte_plot.seek(0)
+            reader = PdfReader(byte_plot)
+            for page in reader.pages:
+                merger.add_page(page)
+
             with alive_bar(
                 1, ctrl_c=False, bar="blocks", title=f"Decompositon Plot:{denovo_name}"
             ) as bar:

{SigProfilerAssignment-0.1.8 → sigprofilerassignment-0.2.0}/SigProfilerAssignment/decomposition.py

@@ -24,7 +24,7 @@ from SigProfilerMatrixGenerator.scripts import CNVMatrixGenerator as scna
 from sigProfilerPlotting import sigProfilerPlotting as sigPlot
 import sigProfilerPlotting
 import os, sys
-from pypdf import PdfMerger
+from pypdf import PdfWriter, PdfReader
 import fitz
 import time
 from pathlib import Path
@@ -93,7 +93,7 @@ def generate_sample_reconstruction(
     project = "test_run"
     mtype = "96"
 
-    final_pdf = PdfMerger()
+    final_pdf = PdfWriter()
     samples = samples_input.copy(deep=True)
     samples.reset_index(inplace=True)
     for sample_name in samples.columns[1:]:
@@ -103,7 +103,7 @@ def generate_sample_reconstruction(
         basis_names = (
             subset[subset["Samples"].str.contains(sample_name)].columns[1:].tolist()
         )
-        recon_tmb = subset.sum(axis=1)
+        recon_tmb = subset.select_dtypes(include=['number']).sum(axis=1)
         weights = []
         for i in range(len(basis_names)):
             weights.append(
@@ -133,7 +133,11 @@ def generate_sample_reconstruction(
             exome=execution_parameters["exome"],
             volume=get_storage_dir(execution_parameters["volume"]),
         )
-        final_pdf.append(result)
+
+        result.seek(0)
+        reader = PdfReader(result)
+        for page in reader.pages:
+            final_pdf.add_page(page)
 
     pdf_output_path = os.path.join(
         output_dir, "Reconstructed_Sample_Plots_" + str(mtype) + ".pdf"

sigprofilerassignment-0.2.0/SigProfilerAssignment/version.py

@@ -0,0 +1,8 @@
+
+# THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
+short_version = '0.2.0'
+version = '0.2.0'
+Update = 'v0.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
+
+    
+    

{SigProfilerAssignment-0.1.8 → sigprofilerassignment-0.2.0/SigProfilerAssignment.egg-info}/PKG-INFO

@@ -1,14 +1,35 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: SigProfilerAssignment
-Version: 0.1.8
+Version: 0.2.0
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
 Author-email: rvangara@health.ucsd.edu
 License: UCSD
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
-Provides-Extra: tests
 License-File: LICENSE.txt
+Requires-Dist: scipy>=1.13
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
+Requires-Dist: sigProfilerPlotting>=1.4.0
+Requires-Dist: reportlab>=3.5.42
+Requires-Dist: pypdf>=5.0.0
+Requires-Dist: alive_progress>=2.4.1
+Requires-Dist: PyMuPDF>=1.21.0
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/mz79v/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)

{SigProfilerAssignment-0.1.8 → sigprofilerassignment-0.2.0}/SigProfilerAssignment.egg-info/SOURCES.txt

@@ -16,7 +16,6 @@ SigProfilerAssignment.egg-info/entry_points.txt
 SigProfilerAssignment.egg-info/not-zip-safe
 SigProfilerAssignment.egg-info/requires.txt
 SigProfilerAssignment.egg-info/top_level.txt
-SigProfilerAssignment/DecompositionPlots/.DS_Store
 SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py
 SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py
 SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py

sigprofilerassignment-0.2.0/SigProfilerAssignment.egg-info/requires.txt

@@ -0,0 +1,12 @@
+scipy>=1.13
+numpy>=2.0.0
+pandas>=2.0.0
+SigProfilerMatrixGenerator>=1.3.0
+sigProfilerPlotting>=1.4.0
+reportlab>=3.5.42
+pypdf>=5.0.0
+alive_progress>=2.4.1
+PyMuPDF>=1.21.0
+
+[tests]
+pytest

{SigProfilerAssignment-0.1.8 → sigprofilerassignment-0.2.0}/setup.py

@@ -6,7 +6,7 @@ import os
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "0.1.8"
+VERSION = "0.2.0"
 
 
 def write_version_py(filename="SigProfilerAssignment/version.py"):
@@ -15,7 +15,7 @@ def write_version_py(filename="SigProfilerAssignment/version.py"):
 # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'v0.1.8: Add Dockerfile and remove uncessary dependencies'
+Update = 'v0.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
 
     
     """
@@ -33,13 +33,13 @@ with open("README.md") as f:
     long_description = f.read()
 
 requirements = [
-    "scipy>=1.6.3",
-    "numpy>=1.21.2,<2.0.0",
-    "pandas>=1.2.4,<2.0.0",
-    "SigProfilerMatrixGenerator>=1.2.28",
-    "sigProfilerPlotting>=1.3.24",
+    "scipy>=1.13",
+    "numpy>=2.0.0",
+    "pandas>=2.0.0",
+    "SigProfilerMatrixGenerator>=1.3.0",
+    "sigProfilerPlotting>=1.4.0",
     "reportlab>=3.5.42",
-    "pypdf>=3.1.0",
+    "pypdf>=5.0.0",
     "alive_progress>=2.4.1",
     "PyMuPDF>=1.21.0",  # required for package "fitz"
 ]
@@ -57,6 +57,7 @@ setup(
     license="UCSD",
     packages=["SigProfilerAssignment"],
     install_requires=requirements,
+    python_requires=">=3.9",
     extras_require={
         "tests": [
             "pytest",

SigProfilerAssignment-0.1.8/SigProfilerAssignment/version.py

@@ -1,8 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
-short_version = '0.1.8'
-version = '0.1.8'
-Update = 'v0.1.8: Add Dockerfile and remove uncessary dependencies'
-
-    
-    

SigProfilerAssignment-0.1.8/SigProfilerAssignment.egg-info/requires.txt

@@ -1,12 +0,0 @@
-scipy>=1.6.3
-numpy<2.0.0,>=1.21.2
-pandas<2.0.0,>=1.2.4
-SigProfilerMatrixGenerator>=1.2.28
-sigProfilerPlotting>=1.3.24
-reportlab>=3.5.42
-pypdf>=3.1.0
-alive_progress>=2.4.1
-PyMuPDF>=1.21.0
-
-[tests]
-pytest