Remove print statements and modifications made to reference signatures

SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_DBS_GRCh37.txt

@@ -1,4 +1,4 @@
-MutationType	DBS1	DBS2	DBS3	DBS4	DBS5	DBS6	DBS7	DBS8	DBS9	DBS10	DBS11
+Type	DBS1	DBS2	DBS3	DBS4	DBS5	DBS6	DBS7	DBS8	DBS9	DBS10	DBS11
 AC>CA	4.97126349633023e-05	0.000374079158890813	0.0063473232068572	0.00414185748142889	0.0021398219882088	0.00266057088135458	0.0458801320676095	0.214923551692663	0.0245918183020509	0.00963041738228935	0.00136990659976803
 AC>CG	2.64067115298024e-05	3.17067094567882e-05	4.64803982864346e-05	4.96222538837858e-05	0.00046196156941704	0.000146031334089387	0.00624729467151545	0.000972654026962609	0.00206931154005063	1.77007671512483e-05	0.00019398677398175
 AC>CT	0.00429109062359289	0.000126026668503322	0.00301872694247382	8.32373290953826e-18	0.0020198319701784	0.000240051508092143	0.0135941132052176	0.317886927619846	0.0284905212035956	0.0135005851153589	0.000755948459434036

SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_ID_GRCh37.txt

@@ -1,4 +1,4 @@
-MutationType	ID1	ID2	ID3	ID4	ID5	ID6	ID7	ID8	ID9	ID10	ID11	ID12	ID13	ID14	ID15	ID16	ID17	ID18
+Type	ID1	ID2	ID3	ID4	ID5	ID6	ID7	ID8	ID9	ID10	ID11	ID12	ID13	ID14	ID15	ID16	ID17	ID18
 1:Del:C:0	0.000159889000761019	0.0048241160289447	0.124727109374181	0.00724971696375141	0.0222021078667874	0.0305067990915204	0.000466560997200634	0.0398275578805173	0.33493987999518	0.0251054140979111	0.00157656499873875	0.052787740788849	0.0655483705411614	0.0120160090841121	0.026527369337078	0.000952768885842137	0.00611759853519847	0.00601204810230084
 1:Del:C:1	0.000773523003681714	2.21000001326e-05	0.208876169626629	0.00273486898632566	0.0285472148287167	0.00549190301647571	1e-18	0.0239159379282522	0.0999942257000173	0.0293063201142946	0.000550317999559745	0.0146746649413013	0.0175364628772448	0.00194623201362362	0.12100978700592	2.63915642267698e-18	0.00366755530652	0.00200401603410028
 1:Del:C:2	3.31000001575451e-18	3.11000001866e-06	0.176324217528973	0.00204106298979469	0.0265969268404184	0.00803399402410198	0.00856194494862833	0.00333055399000834	0.00269065499192804	0.0188040560733358	0.00035733799971413	0.000561931997752272	0.00512021896415847	0.000683696004785872	0.147828864433683	8.1541662061712e-05	0.00122032669693285	0.00200401603410028

SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.3_SBS_GRCh37.txt

@@ -1,4 +1,4 @@
-MutationType	SBS1	SBS2	SBS3	SBS4	SBS5	SBS6	SBS7a	SBS7b	SBS7c	SBS7d	SBS8	SBS9	SBS10a	SBS10b	SBS10c	SBS10d	SBS11	SBS12	SBS13	SBS14	SBS15	SBS16	SBS17a	SBS17b	SBS18	SBS19	SBS20	SBS21	SBS22	SBS23	SBS24	SBS25	SBS26	SBS27	SBS28	SBS29	SBS30	SBS31	SBS32	SBS33	SBS34	SBS35	SBS36	SBS37	SBS38	SBS39	SBS40	SBS41	SBS42	SBS43	SBS44	SBS45	SBS46	SBS47	SBS48	SBS49	SBS50	SBS51	SBS52	SBS53	SBS54	SBS55	SBS56	SBS57	SBS58	SBS59	SBS60	SBS84	SBS85	SBS86	SBS87	SBS88	SBS89	SBS90	SBS91	SBS92	SBS93	SBS94	SBS95
+Type	SBS1	SBS2	SBS3	SBS4	SBS5	SBS6	SBS7a	SBS7b	SBS7c	SBS7d	SBS8	SBS9	SBS10a	SBS10b	SBS10c	SBS10d	SBS11	SBS12	SBS13	SBS14	SBS15	SBS16	SBS17a	SBS17b	SBS18	SBS19	SBS20	SBS21	SBS22	SBS23	SBS24	SBS25	SBS26	SBS27	SBS28	SBS29	SBS30	SBS31	SBS32	SBS33	SBS34	SBS35	SBS36	SBS37	SBS38	SBS39	SBS40	SBS41	SBS42	SBS43	SBS44	SBS45	SBS46	SBS47	SBS48	SBS49	SBS50	SBS51	SBS52	SBS53	SBS54	SBS55	SBS56	SBS57	SBS58	SBS59	SBS60	SBS84	SBS85	SBS86	SBS87	SBS88	SBS89	SBS90	SBS91	SBS92	SBS93	SBS94	SBS95
 A[C>A]A	0.00088615723087747	5.80016751463797e-07	0.0208083233293317	0.0421964976906917	0.011997600479904	0.000425233006425871	6.70435065427006e-05	0.00232938611358363	0.00483040594731581	4.03937995517688e-05	0.0440982184319753	0.000557953689843743	0.00219017006670567	0.000181997452035671	0.00433145266043067	0.0101139695135519	0.000146207934878072	0.00452059219757788	0.00181991985072977	0.00112049160448655	0.000944202153681101	0.0159950367400995	0.00207026139120325	0.000607958306219358	0.0515338577445382	0.00126938219168731	0.000619283396467891	0.000156992630765912	0.00601276346608901	0.000835522871466248	0.0364134001312483	0.00989846573781064	0.000873117958236158	0.00520781844485345	0.000783905147477154	0.0632092620531686	0.00179968073663732	0.0095349845981014	0.022297772452532	0.00311135966417324	0.00486795023758959	0.00882694852389529	0.0251937771370472	0.00395082177092835	0.0127948692574278	0.0117015211977557	0.0282037510988962	0.0021101932937057	0.00116025223883672	0.0295062922168152	7.68194564478318e-18	0.00910813556464992	0.0044	0.0677878741050801	0.000855467975201154	0.0251166272072112	0.11900027370063	0.140963913238211	0.0151962769121565	0.00538350950984947	0.00216035753917248	0.00588112588239664	0.0125974817382056	0.012306325451282	0.0588746191516836	0.00358820822822124	0.0061527065694672	0.00347199473960039	0.00608025719462903	0.00295430070903217	0.00897255127904656	1e-18	0.032168854189218	0.00220164987697197	0.00294455046139974	0.0113293395468264	0.0115732275143254	0.0155796699205714	0.0384083799754225
 A[C>A]C	0.00228040461219034	0.000148004274511452	0.0165066026410564	0.0332972363293847	0.00943811237752452	0.000524287283216839	0.000179116233897663	0.00046087854006955	0.00115009665412281	0.000764882590522354	0.0477980689580141	0.00408966055817367	0.00177013745117308	0.0065399084412818	0.0148302194712279	0.0184460598341763	0.000552786164744493	0.00113014804939447	0.000720968248558332	0.0131057500167623	0.000497106430486766	0.00289910040914304	0.000918115921316223	0.000128991153786673	0.0158103874245379	0.000640688177064223	0.0013906363830216	0.00235988922679969	9.54438660008139e-05	0.000399249851155728	0.0265097555900571	0.00699891516814894	0.000528071342438363	0.0047380152454137	0.00252969390703724	0.0512075034354784	0.00050591025152138	0.0184902741158151	0.0187981220676055	0.00223097493604705	0.00695707056542578	0.0461840341793842	0.00831794546746954	0.00145030166274585	0.0100959515234391	0.00715092962085071	0.0134017824370641	0.00122011176223742	0.0206044794138246	0.00590125844336305	0.000150038000874672	0.00284941672439652	0.0047	0.0296946882141723	0.000841460312449322	0.00703465694289619	0.127000292100672	0.00168956747072749	0.00653839809246734	0.00196127855749163	0.000796131759806155	0.00205039252702604	0.0156968621658593	0.00143073539799457	0.00674709132892809	0.00236881713116555	0.000779342832132512	0.00500730862445185	0.000879937028166784	0.00377450090588022	0.00457257517091682	1e-18	0.0176937280715253	0.000708222617756176	0.0529970882409236	0.00974472961021081	0.00809634412960846	0.0247462165428657	0.0173838367236145
 A[C>A]G	0.000177031410683197	5.23015105199252e-05	0.00175070028011204	0.0155987053074595	0.0018496300739852	5.20285090215183e-05	7.12462338185117e-05	0.000185950994474916	0.000377031685742869	0.000249961630889658	0.00461981335954027	0.00042596464493447	0.000150011648404498	5.34992510104857e-05	0.00065711618103902	0.000726534557978129	9.42340183015523e-05	0.000540070749268154	0.000263988373952011	0.000413181279154416	4.61098721236216e-05	0.00101968359218135	4.76060107349154e-05	5.81960089177081e-05	0.00243159755959666	0.000245880330043368	2.18099806833603e-05	0.000293986200287758	0.000765351755666904	9.85616800472162e-08	0.014805448405013	0.00144977528483085	0.00011401540348101	0.000782672138641121	0.000352957292167647	0.0192028137883044	9.12838062527707e-05	0.00165912729904071	0.0044595544905064	0.000414180997095731	5.19781134198478e-05	0.00138951964305939	0.00223944685662641	0.00106022052586938	0.00189923840539943	0.00267034714512887	0.00292038841165875	6.14056247552276e-05	3.34072627389194e-05	0.000626133522973774	9.16232058674661e-07	0.00165966026754323	3e-04	0.00137975318974942	0.000258141213569471	0.00711470993797893	0.00577001327103052	0.00479877151449229	0.00413898594844263	0.0381248535920567	0.00164027146492725	4.49085972992533e-05	0.000205958828418282	0.00333171250022512	0.000824644495757878	0.000141929127690088	2.23098140648973e-16	0.000452641966051853	0.000306011009795412	0.000385490092517622	0.00620856628748506	1e-18	0.0096708342916345	0.000138565642613613	0.000204200082036665	0.00469656981213721	0.00176062063415735	0.00157427088821657	0.00836014729327226

SigProfilerAssignment/decomposition.py

@@ -45,7 +45,6 @@ def convert_PDF_to_PNG(input_file_name, output_directory, page_names):
 
 # Create sample reconstruction plots
 def generate_sample_reconstruction(cosmic_sigs, samples_input, activities, output_dir):
-    s1 = time.time()
     project = "test_run"
     mtype="96"
 
@@ -80,11 +79,8 @@ def generate_sample_reconstruction(cosmic_sigs, samples_input, activities, outpu
     web_png_path = os.path.join(output_dir,"WebPNGs")
 
     final_pdf.write(pdf_output_path)
-    print("time to generate the pdf: ", time.time() - s1)
 
-    s2 = time.time()
     convert_PDF_to_PNG(pdf_output_path, web_png_path, samples.columns[1:])
-    print("time to convert PDF to PNG: ", time.time() - s2)
 
     return pdf_output_path
 
@@ -660,12 +656,10 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
                 "Assignment_Solution_Activities.txt")
         cosmic_activities = pd.read_csv(acts_path, sep="\t")
         # Create sample reconstruction plots
-        s=time.time()
         generate_sample_reconstruction(cosmic_sig_ref,
                                         genomes,
                                         cosmic_activities,
                                         ss_recon_odir)
-        print("generate_sample_reconstruction total time: ", time.time() - s)
 
     # Complete JOB_METADATA
     sysdata = open(output+"/JOB_METADATA.txt", "a")