Merge pull request #46 from AlexandrovLab/development

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AlexandrovLab · Oct 19, 2022 · 9e0894b · 9e0894b
2 parents 3095567 + cf1ccae
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diff --git a/README.md b/README.md
@@ -28,7 +28,7 @@ Unzip the contents of SigProfilerExtractor-master.zip or the zip file of a corre
 $ cd SigProfilerAssignment-master
 $ pip install .
 ```
-## Signature Subtypes
+## Signature Subgroups
 ```python
 exclude_signature_subgroups = ['remove_MMR_deficiency_signatures',
                                'remove_POL_deficiency_signatures',
@@ -47,22 +47,22 @@ exclude_signature_subgroups = ['remove_MMR_deficiency_signatures',
 ```
 
 
-| Signature Subgroup      | SBS Signatures that are excluded |
-| ----------- | ----------- |
-|MMR_deficiency_signatures|	6, 14, 15, 20, 21, 26, 44|
-|POL_deficiency_signatures|	10a, 10b, 10c, 10d, 28|
-|HR_deficiency_signatures|	3|
-|BER_deficiency_signatures|	30, 36|
-|Chemotherapy_signatures|	11, 25, 31, 35, 86, 87, 90|
-|Immunosuppressants_signatures|	32|
-|Treatment_signatures|	11, 25, 31, 32, 35, 86, 87, 90|
-|APOBEC_signatures|	2, 13|
-|Tobacco_signatures	|4, 29, 92|
-|UV_signatures|	7a, 7b, 7c, 7d, 38|
-|AA_signatures|	22|
-|Colibactin_signatures|	88|
-|Artifact_signatures|	27, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95|
-|Lymphoid_signatures|	9, 84, 85|
+|Signature subgroup |           SBS signatures excluded | DBS signatures excluded | ID signatures excluded |
+| ----------- | ----------- | ----------- | ----------- |
+|MMR_deficiency_signatures|     6, 14, 15, 20, 21, 26, 44|      7, 10|  7|
+|POL_deficiency_signatures|     10a, 10b, 10c, 10d, 28|         3|      -|
+|HR_deficiency_signatures|      3|                              -|      6|
+|BER_deficiency_signatures|     30, 36|                         -|      -|
+|Chemotherapy_signatures|       11, 25, 31, 35, 86, 87, 90|     5|      -|
+|Immunosuppressants_signatures| 32|                             -|      -|
+|Treatment_signatures|          11, 25, 31, 32, 35, 86, 87, 90| 5|      -|
+|APOBEC_signatures|             2, 13|                          -|      -|
+|Tobacco_signatures |           4, 29, 92|                      2|      3|
+|UV_signatures|                 7a, 7b, 7c, 7d, 38|             1|      13|
+|AA_signatures|                 22|                             -|      -|
+|Colibactin_signatures|         88|                             -|      18|
+|Artifact_signatures|           27, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95|-|-|
+|Lymphoid_signatures|           9, 84, 85|                      -|      -|
 
 <!-- 
 ```python
@@ -132,10 +132,11 @@ Analyze.cosmic_fit( samples,
 | **genome_build** | 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. |
 | **cosmic_version** | Float | Takes a positive float among 1, 2, 3, 3.1, 3.2 and 3.3. Defines the version of the COSMIC reference signatures. The default value is 3.3. |
 | **new_signature_thresh_hold**| Float | Parameter in cosine similarity to declare a new signature. Applicable for decompose_fit only. The default value is 0.8. |
-| **make_plots** | Boolean | Toggle on and off for making and saving all plots. Default value is True. |
-| **exclude_signature_subgroups** | List | Removes the signatures corresponding to specific subtypes for better fitting. The usage is given above. Default value is None. |
+| **exclude_signature_subgroups** | List | Removes the signatures corresponding to specific subtypes for better fitting. The usage is given above. The default value is None. |
 | **exome** | Boolean | Defines if the exome renormalized signatures will be used. The default value is False. |
-| **verbose** | Boolean | Prints statements. Default value is False. |
+| **export_probabilities** | Boolean | Defines if the probability matrix is created. The default value is True. |
+| **make_plots** | Boolean | Toggle on and off for making and saving all plots. The default value is True. |
+| **verbose** | Boolean | Prints statements. The default value is False. |
 
 
         

diff --git a/SigProfilerAssignment/Analyzer.py b/SigProfilerAssignment/Analyzer.py
@@ -1,11 +1,11 @@
 from SigProfilerAssignment import decomposition as decomp
 
-def decompose_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96"):
+def decompose_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96",export_probabilities=True):
 
-                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= True,denovo_refit_option=False,cosmic_fit_option=False,devopts=devopts,new_signature_thresh_hold=new_signature_thresh_hold,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type)
+                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= True,denovo_refit_option=False,cosmic_fit_option=False,devopts=devopts,new_signature_thresh_hold=new_signature_thresh_hold,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities)
 
-def denovo_fit(samples,  output, signatures=None, signature_database=None,nnls_add_penalty=0.05,nnls_remove_penalty=0.01, initial_remove_penalty=0.05, genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,input_type='matrix',context_type="96"):
-                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, new_signature_thresh_hold=new_signature_thresh_hold, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=True,cosmic_fit_option=False,devopts=devopts,input_type=input_type,context_type=context_type)
+def denovo_fit(samples,  output, signatures=None, signature_database=None,nnls_add_penalty=0.05,nnls_remove_penalty=0.01, initial_remove_penalty=0.05, genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,input_type='matrix',context_type="96",export_probabilities=True):
+                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, new_signature_thresh_hold=new_signature_thresh_hold, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=True,cosmic_fit_option=False,devopts=devopts,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities)
 
-def cosmic_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96"):
-                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=False,cosmic_fit_option=True,devopts=devopts,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type)
+def cosmic_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96",export_probabilities=True):
+                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=False,cosmic_fit_option=True,devopts=devopts,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities)
diff --git a/SigProfilerAssignment/decompose_subroutines.py b/SigProfilerAssignment/decompose_subroutines.py
@@ -169,7 +169,7 @@ def get_items_from_index(x,y):
             pass
     return z
 
-def signature_decomposition(signatures, mtype, directory, genome_build="GRCh37", cosmic_version=3.3,signature_database=None, add_penalty=0.05, remove_penalty=0.01, mutation_context=None, connected_sigs=True, make_decomposition_plots=True, originalProcessAvg=None,new_signature_thresh_hold=0.8,sig_exclusion_list=[],exome=False):
+def signature_decomposition(signatures, mtype, directory, genome_build="GRCh37", cosmic_version=3.3,signature_database=None, add_penalty=0.05, remove_penalty=0.01, mutation_context=None, connected_sigs=True, make_decomposition_plots=True, originalProcessAvg=None,new_signature_thresh_hold=0.8,sig_exclusion_list=[],exome=False, m_for_subgroups='SBS'):
 
     originalProcessAvg = originalProcessAvg.reset_index()
     if not os.path.exists(directory+"/Solution_Stats"):
@@ -236,7 +236,7 @@ def signature_decomposition(signatures, mtype, directory, genome_build="GRCh37",
         except:
             sys.exit("Wrong format of signature database for decompose_fit, Please pass a text file of signatures in the format of COSMIC sig database")
 
-    sig_exclusion_list= ['SBS'+items for items in sig_exclusion_list]
+    sig_exclusion_list= [m_for_subgroups+items for items in sig_exclusion_list]
     lognote.write("The following signatures are excluded: "+" ".join(str(item) for item in sig_exclusion_list))
     sigDatabase.drop(sig_exclusion_list, axis=1, inplace=True,errors='ignore')
     signames=sigDatabase.columns
@@ -772,19 +772,21 @@ def make_final_solution(processAvg, allgenomes, allsigids, layer_directory, m, i
         else:
             custom_signatures_plot(processes, layer_directory+"/Signatures")
 
-    probability = probabilities(processAvg, exposureAvg, index, allsigids, allcolnames)
-    probability=probability.set_index("Sample Names" )
+    if export_probabilities==True:
+
+        probability = probabilities(processAvg, exposureAvg, index, allsigids, allcolnames)
+        probability=probability.set_index("Sample Names" )
+
+        if cosmic_sigs==False:
+
+            if refit_denovo_signatures==True:
+                probability.to_csv(layer_directory+"/Activities"+"/"+"De_Novo_Mutation_Probabilities_refit.txt", "\t") 
+            else:
+                probability.to_csv(layer_directory+"/Activities"+"/"+"De_Novo_Mutation_Probabilities.txt", "\t") 
+        if cosmic_sigs==True:
+            probability.to_csv(layer_directory+"/Activities"+"/"+"Decomposed_Mutation_Probabilities.txt", "\t") 
 
-    if cosmic_sigs==False:
-
-        if refit_denovo_signatures==True:
-            probability.to_csv(layer_directory+"/Activities"+"/"+"De_Novo_Mutation_Probabilities_refit.txt", "\t") 
-        else:
-            probability.to_csv(layer_directory+"/Activities"+"/"+"De_Novo_Mutation_Probabilities.txt", "\t") 
-    if cosmic_sigs==True:
-        probability.to_csv(layer_directory+"/Activities"+"/"+"Decomposed_Mutation_Probabilities.txt", "\t") 
 
-
     return exposures
 ################################################################### FUNCTION ONE ###################################################################
 #function to calculate multiple similarities/distances