SigProfilerAssignment 0.2.5__tar.gz → 0.2.6__tar.gz

{sigprofilerassignment-0.2.5/SigProfilerAssignment.egg-info → sigprofilerassignment-0.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerAssignment
-Version: 0.2.5
+Version: 0.2.6
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
@@ -15,7 +15,7 @@ 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: pypdf>=6.0.0
 Requires-Dist: alive_progress>=2.4.1
 Requires-Dist: pdf2image>=1.16.0
 Provides-Extra: tests

{sigprofilerassignment-0.2.5 → sigprofilerassignment-0.2.6}/SigProfilerAssignment/decompose_subroutines.py

@@ -40,19 +40,13 @@ def getProcessAvg(
 ):
     paths = spa.__path__[0]
 
-    if (
-        genome_build == "GRCh37"
-        or genome_build == "GRCh38"
-        or genome_build == "mm9"
-        or genome_build == "mm10"
-        or genome_build == "rn6"
-    ):
+    if genome_build in ["GRCh37", "GRCh38", "mm9", "mm10", "mm39", "rn6", "rn7"]:
         genome_build = genome_build
     else:
         print(
             "The selected genome build is "
             + str(genome_build)
-            + ". COSMIC signatures are available only for GRCh37/38, mm9/10 and rn6 genomes. So, the genome build is reset to GRCh37."
+            + ". COSMIC signatures are available only for GRCh37/38, mm9/10/39 and rn6/7 genomes. So, the genome build is reset to GRCh37."
         )
         genome_build = "GRCh37"
     if samples.shape[0] == 96:

{sigprofilerassignment-0.2.5 → sigprofilerassignment-0.2.6}/SigProfilerAssignment/decomposition.py

@@ -271,7 +271,7 @@ def spa_analyze(
         activities: A string. Path to a tab delimilted file that contains the activity table where the rows are sample IDs and colunms are signature IDs.
         samples: A string. Path to a tab delimilted file that contains the activity table where the rows are mutation types and colunms are sample IDs.
         output: A string. Path to the output folder.
-        genome_build = A string. The reference genome build. List of supported genomes: "GRCh37", "GRCh38", "mm9", "mm10" and "rn6". The default value is "GRCh37". If the selected genome is not in the supported list, the default genome will be used.
+        genome_build = A string. The reference genome build. List of supported genomes: "GRCh37", "GRCh38", "mm9", "mm10", "mm39", "rn6", and "rn7". The default value is "GRCh37". If the selected genome is not in the supported list, the default genome will be used.
         verbose = Boolean. Prints statements. Default value is False.
         exome = Boolean. Defines if the exome renormalized signatures will be used. The default value is False.
         sample_reconstruction_plots (str): Select output format for sample reconstruction plots. Valid options are {'pdf', 'png', 'both', 'none'}. Default is 'none'.

sigprofilerassignment-0.2.6/SigProfilerAssignment/version.py

@@ -0,0 +1,7 @@
+
+# THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
+short_version = '0.2.6'
+version = '0.2.6'
+Update = 'v0.2.6:  Support for assigning signatures for rn7 and mm39 genomes.'
+
+    

{sigprofilerassignment-0.2.5 → sigprofilerassignment-0.2.6/SigProfilerAssignment.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerAssignment
-Version: 0.2.5
+Version: 0.2.6
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
@@ -15,7 +15,7 @@ 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: pypdf>=6.0.0
 Requires-Dist: alive_progress>=2.4.1
 Requires-Dist: pdf2image>=1.16.0
 Provides-Extra: tests

{sigprofilerassignment-0.2.5 → sigprofilerassignment-0.2.6}/SigProfilerAssignment.egg-info/requires.txt

@@ -4,7 +4,7 @@ pandas>=2.0.0
 SigProfilerMatrixGenerator>=1.3.0
 sigProfilerPlotting>=1.4.0
 reportlab>=3.5.42
-pypdf>=5.0.0
+pypdf>=6.0.0
 alive_progress>=2.4.1
 pdf2image>=1.16.0
 

{sigprofilerassignment-0.2.5 → sigprofilerassignment-0.2.6}/setup.py

@@ -6,7 +6,7 @@ import os
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "0.2.5"
+VERSION = "0.2.6"
 
 
 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 = 'v0.2.5:  Support for generating decomposition plots for custom signature sets.'
+Update = 'v0.2.6:  Support for assigning signatures for rn7 and mm39 genomes.'
 
     """
     fh = open(filename, "w")
@@ -38,7 +38,7 @@ requirements = [
     "SigProfilerMatrixGenerator>=1.3.0",
     "sigProfilerPlotting>=1.4.0",
     "reportlab>=3.5.42",
-    "pypdf>=5.0.0",
+    "pypdf>=6.0.0",
     "alive_progress>=2.4.1",
     "pdf2image>=1.16.0",  # replacing PyMuPDF
     # Note: 'poppler' is required as a system dependency for pdf2image

sigprofilerassignment-0.2.5/SigProfilerAssignment/version.py

@@ -1,7 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
-short_version = '0.2.5'
-version = '0.2.5'
-Update = 'v0.2.5:  Support for generating decomposition plots for custom signature sets.'
-
-