Merge pull request #114 from AlexandrovLab/spa_r_i1

v0.1.2: Spa_r_i1

Author: mdbarnesUCSD

SigProfilerAssignment/decomposition.py

@@ -24,6 +24,7 @@
     SigProfilerMatrixGeneratorFunc as datadump,
 )
 from SigProfilerMatrixGenerator.scripts import CNVMatrixGenerator as scna
+from sigProfilerPlotting import sigProfilerPlotting as sigPlot
 import sigProfilerPlotting
 import os, sys
 from PyPDF2 import PdfMerger
@@ -302,6 +303,9 @@ def spa_analyze(
     mutation_type = str(genomes.shape[0])
     m = mutation_type
 
+    # Re-indexing the input matrix file by using process_input function from SigProfilePlotting
+    genomes = sigPlot.process_input(genomes, m)
+
     m_for_subgroups = ""
     if m == "96" or m == "288" or m == "1536":
         m_for_subgroups = "SBS"

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "0.1.1"
+VERSION = "0.1.2"
 
 
 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 = 'v0.1.1: Update cosmic fit and decompose fit to use SV COSMIC signatures.'
+Update = 'v0.1.2: Add matrix input format processing'
 
     
     """