Add filtering for only exome mutations

Author: marcos-diazg

SigProfilerAssignment/decompose_subroutines.py

@@ -480,7 +480,7 @@ def signature_decomposition(signatures, mtype, directory, genome_build="GRCh37",
 def make_final_solution(processAvg, allgenomes, allsigids, layer_directory, m, index, allcolnames, process_std_error = "none", signature_stabilities = " ", \
                         signature_total_mutations= " ", signature_stats = "none",  cosmic_sigs=False, attribution= 0, denovo_exposureAvg  = "none", add_penalty=0.05, \
                         remove_penalty=0.01, initial_remove_penalty=0.05, de_novo_fit_penalty=0.02, background_sigs=0, genome_build="GRCh37", sequence="genome", export_probabilities=True, export_probabilities_per_mutation=False, \
-                        refit_denovo_signatures=True, collapse_to_SBS96=True, connected_sigs=True, pcawg_rule=False, verbose=False,make_plots = True, samples='./', input_type='matrix', denovo_refit_option=True):
+                        refit_denovo_signatures=True, collapse_to_SBS96=True, connected_sigs=True, pcawg_rule=False, verbose=False,make_plots = True, samples='./', input_type='matrix', denovo_refit_option=True, exome=False):
 
     if processAvg.shape[0]==allgenomes.shape[0] and processAvg.shape[0] != 96:
         collapse_to_SBS96=False
@@ -794,7 +794,7 @@ def make_final_solution(processAvg, allgenomes, allsigids, layer_directory, m, i
         if export_probabilities==True:
             if input_type=='vcf':
                 if m=='96' or m=='78' or m=='83':
-                    probability_per_mutation, samples_prob_per_mut = probabilities_per_mutation(probability, samples, m)
+                    probability_per_mutation, samples_prob_per_mut = probabilities_per_mutation(probability, samples, m, exome)
 
                     if denovo_refit_option==True:
                         if refit_denovo_signatures==True:
@@ -941,7 +941,7 @@ def probabilities(W, H, index, allsigids, allcolnames):
 
 
 ################################################### Generation of probabilities for each processes given to A mutation ############################################
-def probabilities_per_mutation(probability_matrix, samples_path, m):  
+def probabilities_per_mutation(probability_matrix, samples_path, m, exome=False):  
 #
     probability_matrix=probability_matrix.reset_index()
 #
@@ -963,12 +963,15 @@ def probabilities_per_mutation(probability_matrix, samples_path, m):
 #
     all_mutations = pd.DataFrame()
     for file in seqinfo_files:
-        if 'exome' not in file:
+        if 'exome' in file:
+            exome_df = pd.read_csv(seqinfo_path + file, sep='\t',header=None)
+        else:
             try:
                 new = pd.read_csv(seqinfo_path + file, sep='\t',header=None)
                 all_mutations = pd.concat([all_mutations, new])
             except (pd.errors.EmptyDataError):
                 pass
+
     all_mutations[3] = all_mutations[3].str[interval_low:interval_high]
     if m=='96' or m=='78':
         del all_mutations[4]
@@ -978,6 +981,14 @@ def probabilities_per_mutation(probability_matrix, samples_path, m):
         del all_mutations[4]
 
     all_mutations.columns = ['Sample Names', 'Chr', 'Pos', 'MutationType']
+    if exome==True:
+        del exome_df[2]
+        del exome_df[3]
+        del exome_df[4]
+        exome_df.columns = ['Chr', 'Pos']
+        exome_df['Chr'] = [str(x) for x in (exome_df['Chr']).to_list()]
+        all_mutations['Chr'] = [str(x) for x in (all_mutations['Chr']).to_list()]
+        all_mutations = pd.merge(all_mutations, exome_df)
 #
     all_samples_mutations = [y for x, y in all_mutations.groupby('Sample Names')]
 #

SigProfilerAssignment/decomposition.py

@@ -412,7 +412,7 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
                                     add_penalty=nnls_add_penalty, remove_penalty=nnls_remove_penalty,
                                     initial_remove_penalty=init_rem_denovo,connected_sigs=connected_sigs,refit_denovo_signatures=False,
                                     make_plots=make_plots,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation,
-                                    samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option)
+                                    samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option, exome=exome)
 
         else:
             signature_stabilities=devopts['signature_stabilities']
@@ -426,7 +426,7 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
                                     background_sigs=background_sigs, verbose=verbose, genome_build=genome_build, signature_total_mutations = signature_total_mutations,
                                     add_penalty=nnls_add_penalty, remove_penalty=nnls_remove_penalty, process_std_error = processSTE, signature_stabilities = signature_stabilities,
                                     initial_remove_penalty=init_rem_denovo,connected_sigs=connected_sigs,refit_denovo_signatures=True,export_probabilities=export_probabilities,
-                                    export_probabilities_per_mutation=export_probabilities_per_mutation, samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option)
+                                    export_probabilities_per_mutation=export_probabilities_per_mutation, samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option, exome=exome)
 
         if make_metadata:
             with open(os.path.join(output,"JOB_METADATA_SPA.txt"),"a") as sysdata:
@@ -541,7 +541,7 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
                                 make_plots=make_plots,
                                 export_probabilities=export_probabilities,
                                 export_probabilities_per_mutation=export_probabilities_per_mutation,
-                                samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option)
+                                samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option, exome=exome)
 
         if make_metadata:
             with open(os.path.join(output,"JOB_METADATA_SPA.txt"),"a") as sysdata:
@@ -659,7 +659,7 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
                             make_plots =make_plots,
                             export_probabilities=export_probabilities,
                             export_probabilities_per_mutation=export_probabilities_per_mutation,
-                            samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option)
+                            samples=samples, input_type=input_type, denovo_refit_option=denovo_refit_option, exome=exome)
         if make_metadata:
             with open(os.path.join(output,"JOB_METADATA_SPA.txt"),"a") as sysdata:
                 current_time_end = datetime.datetime.now()