Merge pull request #218 from AlexandrovLab/i4608

I4608
AlexandrovLab · Sep 15, 2023 · e807db2 · e807db2
2 parents ea54ec2 + 8418de1
commit e807db2
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Showing 4 changed files with 16 additions and 16 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -1,9 +1,6 @@
 dist: xenial
 language: python
 
-vm:
-  size: 2x-large
-
 python:
   - '3.8'
 

diff --git a/SigProfilerExtractor/sigpro.py b/SigProfilerExtractor/sigpro.py
@@ -490,7 +490,7 @@ def sigProfilerExtractor(input_type,
             mtypes = ["CNV48"]
         elif mtypes[0]=="32":
             mtypes = ["SV32"]
-        elif mtypes[0]=="96" or "288" or "384" or "1536":
+        elif mtypes[0]=="96" or "288" or "384" or "1536" or "4608":
             mtypes = ["SBS"+mtypes[0]]
         else:
             mtypes = ["CH"+mtypes[0]]
@@ -608,7 +608,7 @@ def sigProfilerExtractor(input_type,
 
             if m.startswith("SBS"):
                 mutation_type = m
-            elif m in ["96","288","384","1536"]:
+            elif m in ["96","288","384","1536", "4608"]:
                 mutation_type="SBS"+m
             elif m.startswith("78"): 
                 mutation_type="DBS78"

diff --git a/SigProfilerExtractor/subroutines.py b/SigProfilerExtractor/subroutines.py
@@ -1095,19 +1095,22 @@ def export_information(loopResults, mutation_type, output, index, colnames, sequ
 
 
     if m=="DBS78":        
-        plot.plotDBS(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot" , "S"+str(i), "78", True, custom_text_upper=stability_list, custom_text_middle=total_mutation_list)
+        plot.plotDBS(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot/" , "S"+str(i), "78", True, custom_text_upper=stability_list, custom_text_middle=total_mutation_list)
     elif m=="ID83":
-        plot.plotID(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot" , "S"+str(i), "83", True, custom_text_upper=stability_list, custom_text_middle=total_mutation_list)
+        plot.plotID(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot/" , "S"+str(i), "83", True, custom_text_upper=stability_list, custom_text_middle=total_mutation_list)
     elif m=="CNV48":
-         plot.plotCNV(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot"  , "S"+str(i), "pdf", percentage=True, aggregate=False)
+         plot.plotCNV(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot/"  , "S"+str(i), "pdf", percentage=True, aggregate=False)
     elif m=="SV32":
-         plot.plotSV(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot"  , "S"+str(i), "pdf", percentage=True, aggregate=False)
-    elif m=="SBS96" or m=="SBS288" or m=="SBS384" or m=="SBS1536" or m=="4608":
+         plot.plotSV(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot/"  , "S"+str(i), "pdf", percentage=True, aggregate=False)
+    elif m=="SBS96" or m=="SBS288" or m=="SBS384" or m=="SBS1536" or m=="SBS4608":
         # parse 'm' to be accepted by the plotSBS function
         tmp_m = m
         if m.startswith("SBS"):
             tmp_m = m[3:]
-        plot.plotSBS(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot", "S"+str(i), tmp_m, True, custom_text_upper=stability_list, custom_text_middle=total_mutation_list)
+        if m=="SBS96" or m=="SBS288" or m=="SBS384" or m=="SBS1536":
+            plot.plotSBS(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot/", "S"+str(i), tmp_m, True, custom_text_upper=stability_list, custom_text_middle=total_mutation_list)
+        elif m=="SBS4608":
+            plot.plotSBS(signature_subdirectory+"/"+mutation_type+"_S"+str(i)+"_Signatures"+".txt", signature_subdirectory+"/Signature_plot/", "S"+str(i), tmp_m, True)
     else:
         custom_signatures_plot(processes, signature_subdirectory)
 

diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = '1.1.21'
+VERSION = '1.1.22'
 
 
 with open('README.md') as f:
@@ -20,7 +20,7 @@ def write_version_py(filename='SigProfilerExtractor/version.py'):
 # THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'Upgrade v1.1.21: Resolve plotSBS context issue.'
+Update = 'Upgrade v1.1.22: Resolve issue with 4608 plotting as custom'
     
     """
     fh = open(filename, 'w')
@@ -32,9 +32,9 @@ def write_version_py(filename='SigProfilerExtractor/version.py'):
           'numpy>=1.21.2',
           'pandas>=1.2.4', 
           'nimfa>=1.1.0', 
-          'SigProfilerMatrixGenerator>=1.2.12', 
-          'sigProfilerPlotting>=1.3.10',
-          'SigProfilerAssignment>=0.0.25',
+          'SigProfilerMatrixGenerator>=1.2.17',
+          'sigProfilerPlotting>=1.3.16',
+          'SigProfilerAssignment>=0.0.32',
           'pillow',
           'statsmodels>=0.9.0',
           'scikit-learn>=0.24.2',