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Merge pull request #64 from AlexandrovLab/development
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@mdbarnesUCSD
mdbarnesUCSD authored Dec 15, 2022
2 parents 8393018 + f690444 commit 5b1b3cd
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Showing 8 changed files with 383 additions and 76 deletions.
11 changes: 8 additions & 3 deletions SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,12 +68,17 @@ def install_cosmic_plots(context_type="96", genome_build="GRCh37", cosmic_versio
context_type_str = ""
if context_type in SBS_CONTEXTS:
context_type_str="SBS"
# the mtype of the cosmic reference signatures to be plotted
cosmic_mtype = "96"
elif context_type in DBS_CONTEXTS:
context_type_str="DBS"
cosmic_mtype = "78"
elif context_type in ID_CONTEXTS:
context_type_str="ID"
cosmic_mtype="83"
elif context_type in CNV_CONTEXTS:
context_type_str="CNV"
cosmic_mtype="48"
else:
raise ValueError("ERROR: context", context_type, "not in context lists.")

Expand Down Expand Up @@ -110,15 +115,15 @@ def install_cosmic_plots(context_type="96", genome_build="GRCh37", cosmic_versio
# Create the respective plots
if context_type_str == "SBS":
cosmic_buff_plots = sigPlt.plotSBS(cosmic_file_path, "buffer",
"buffer", context_type, percentage=True,
"buffer", cosmic_mtype, percentage=True,
savefig_format="buffer_stream")
elif context_type_str == "DBS":
cosmic_mtx = pd.read_csv(cosmic_file_path, sep="\t")
cosmic_buff_plots = mPlt.plotDBS(cosmic_mtx, "buffer",
"buffer", context_type, percentage=True)
"buffer", cosmic_mtype, percentage=True)
elif context_type_str == "ID":
cosmic_buff_plots = sigPlt.plotID(cosmic_file_path, "buffer",
"buffer", context_type, percentage=True,
"buffer", cosmic_mtype, percentage=True,
savefig_format="buffer_stream")

# Process the plots to be stored in JSON file
Expand Down
79 changes: 79 additions & 0 deletions SigProfilerAssignment/data/tests/txt_input/DBS78_S3_Signatures.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,79 @@
MutationType DBS78A DBS78B DBS78C
AC>CA 0.007701220471381021 0.00796216114319705 0.007981890587439242
AC>CG 0.0007596243517717482 0.002515560326185664 0.0032925101545001213
AC>CT 0.0036613791290898232 0.006457311882861631 0.0005561331295132277
AC>GA 0.01430362708112881 0.004434696912948084 0.0015997318608089728
AC>GG 0.0003926123239332924 0.00173157614722669 0.0017389119426070466
AC>GT 0.0008538928064714923 0.002402596564204487 0.00016100885088235373
AC>TA 0.010165360175251478 0.01805363717697631 0.00261797641165181
AC>TG 0.003114907060125063 0.00197977774060746 0.00015713617513952728
AC>TT 0.004272030978231065 0.014490832900833297 0.013703172781998419
AT>CA 0.0027928892339326517 0.005014161980007969 0.002396070483326582
AT>CC 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
AT>CG 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
AT>GA 0.0036192576861408554 0.002549266927125657 0.0016435109142051373
AT>GC 0.0010602097517692498 0.004418470850915384 0.0025812379512018422
AT>TA 0.003956944258188173 0.004084817962978775 0.0001464684126683835
CC>AA 0.21314640432596207 0.08451294089051999 0.022680382505059243
CC>AG 0.03887067049741745 0.04115427631821149 0.009024048910502885
CC>AT 0.07720620729029179 0.02485734054481213 0.025968508956292345
CC>GA 0.023582828800030313 0.027870366043960076 0.001638610521578423
CC>GG 0.003562674971485649 0.00568987110601455 2.1735016235240323e-05
CC>GT 0.003930783755814211 0.015718642590940204 0.05339775148914164
CC>TA 0.013517297922466014 0.004533098282206893 0.045496224127709865
CC>TG 0.003170541205720987 0.006839938957640328 0.01209664115200809
CC>TT 0.016128143786513078 0.014246139319031386 0.22298941016197205
CG>AT 0.0013718631220203292 0.0011760079401392431 1.7845207239020055e-06
CG>GC 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
CG>GT 0.00244295303258383 0.0020108300834782255 0.0015472748098332545
CG>TA 0.0017933385741020302 0.008381587506090043 0.006580830589914228
CG>TC 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
CG>TT 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
CT>AA 0.03056176378391683 0.01997418589716858 0.014524588637995066
CT>AC 0.008723678147525789 0.003198001274002422 7.50284031519044e-05
CT>AG 0.013967309792793117 0.025800739544212945 0.0020262911179308334
CT>GA 0.005183126077014322 0.005399140253827568 8.386640411117696e-07
CT>GC 0.0011205850666285145 0.004794350164159482 0.00952861013530196
CT>GG 0.0026496872936636116 0.004470084855030052 0.0068601189660286365
CT>TA 0.011580483981152839 0.006724140149601681 0.06253116527572274
CT>TC 0.0019991406158068516 0.004034618152533622 0.018667166766935566
CT>TG 0.0026804885171711136 0.012512132214973519 0.005324414347138884
GC>AA 0.056321645556017756 0.035954596747932895 0.026027616262435913
GC>AG 0.03144276377046481 0.013247568246537184 0.018993127785347355
GC>AT 0.009880461198020498 0.018659071143346466 0.003851905400881277
GC>CA 0.0029758732128375696 0.012250714755683133 0.009420340201444902
GC>CG 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
GC>TA 0.00316298710677799 0.003422101290155979 0.002100860018768316
TA>AT 0.005734449959326184 0.011952467915392048 0.009257008301459422
TA>CG 0.0007861925772184009 0.005441112469664091 0.0011438208288380026
TA>CT 0.006876101513741446 0.025988213105597565 0.0024125996946382598
TA>GC 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
TA>GG 0.00024249189863411401 0.0024103037500398726 0.0013367920215785034
TA>GT 0.007528789849845338 0.004463364520623046 0.0016972196946919383
TC>AA 0.07732148085199242 0.1153389820549637 0.010312519165380394
TC>AG 0.006505565074627384 0.011100985203830476 0.043834781590849164
TC>AT 0.04132318901642065 0.019512885481713056 0.15823206782341004
TC>CA 0.028291178711286308 0.027361288188176333 0.006357050018573176
TC>CG 0.0029052182855502195 0.006183057717145459 0.0036399856793170216
TC>CT 0.01686263663632209 0.013389183012335763 0.02573391613084823
TC>GA 0.026104632933950142 0.014143300859971645 0.0014059993330974051
TC>GG 0.003586786781782152 0.0030271233733323412 0.011144287357381301
TC>GT 0.0036715797787563887 0.009821995376649255 0.011928020248677527
TG>AA 0.0065388134503416495 0.005143008082823428 8.142797032206772e-07
TG>AC 0.0018270534210728328 0.0005837329443659201 0.00015887843392647482
TG>AT 0.02519220345420763 0.039821385081496886 0.00022868747462989592
TG>CA 0.018736756909435145 0.03308783940384604 0.018223067678340144
TG>CC 0.0042682058809865 0.0107843768620981 0.02108467224713209
TG>CT 0.04684039905501322 0.08024291258878975 0.0043120405150775705
TG>GA 0.0014536534275289492 0.007176250557132562 0.00046808720675130646
TG>GC 0.0012626774567567622 0.007148928862622767 0.0014375691987117988
TG>GT 0.009330823977628029 0.012159672317460632 0.013992152198510872
TT>AA 0.010670310902712287 0.026377604990301933 0.01347970358558264
TT>AC 0.0006257683793654678 0.002273213075085323 3.7143987795502654e-05
TT>AG 0.0026620588464987094 0.009727526421825346 0.003072377364968748
TT>CA 0.000705486348334734 0.0019214185494595881 0.004295104562746416
TT>CC 0.001428910197188884 0.00024337726569910955 0.005700639425011218
TT>CG 0.0007138851010122948 0.003913518652468753 0.003164384795367994
TT>GA 1.6802229868062568e-06 2.8397882294939336e-06 2.5854232899291676e-06
TT>GC 0.0004692392193969397 0.004688904073969696 0.001783702708067949
TT>GG 0.001892356698820663 0.00102200061695072 0.00015319283604924293
79 changes: 79 additions & 0 deletions SigProfilerAssignment/data/tests/txt_input/sample_matrix_DBS.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,79 @@
MutationType PD3851a PD3890a PD3904a PD3905a PD3945a PD4005a PD4006a PD4085a PD4086a PD4088a PD4103a PD4107a PD4109a PD4115a PD4116a PD4120a PD4192a PD4194a PD4198a PD4199a PD4248a
AC>CA 0 1 1 1 0 0 1 0 0 0 0 0 1 0 1 0 0 0 0 1 0
AC>CG 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0
AC>CT 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0
AC>GA 0 0 0 1 2 0 1 1 0 0 0 0 0 0 3 0 0 0 0 0 0
AC>GG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
AC>GT 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
AC>TA 0 0 0 0 0 2 0 0 0 0 2 0 0 2 2 0 1 0 0 0 1
AC>TG 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
AC>TT 0 1 1 0 2 1 0 0 0 0 0 0 1 1 0 2 0 0 0 0 0
AT>CA 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0
AT>CC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
AT>CG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
AT>GA 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0
AT>GC 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
AT>TA 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0
CC>AA 2 2 13 10 17 3 13 0 1 0 0 23 2 14 21 3 1 0 1 1 2
CC>AG 0 2 2 1 4 5 2 0 0 0 0 5 3 3 2 1 0 0 0 0 0
CC>AT 0 2 3 0 5 3 6 0 0 0 0 10 1 3 9 3 0 0 1 2 0
CC>GA 0 1 1 0 1 1 2 1 0 0 0 4 1 4 1 0 1 0 0 0 1
CC>GG 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
CC>GT 1 2 0 1 1 0 0 0 1 1 1 1 1 0 0 4 0 1 1 1 1
CC>TA 0 1 0 0 1 2 1 0 0 0 0 1 0 0 4 7 0 0 0 1 0
CC>TG 0 1 0 0 0 1 0 0 0 0 0 0 0 1 1 2 0 0 0 0 0
CC>TT 0 2 2 1 3 1 1 1 0 1 2 7 2 2 1 31 0 0 1 5 0
CG>AT 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CG>GC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CG>GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0
CG>TA 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 0 1 0 0
CG>TC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CG>TT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CT>AA 2 1 2 1 2 2 3 0 0 0 0 1 1 1 3 2 0 0 0 0 1
CT>AC 0 0 0 0 1 0 0 0 0 0 0 2 0 1 1 0 0 0 0 0 0
CT>AG 0 0 2 0 2 2 0 0 0 0 3 2 1 3 0 0 0 0 0 0 0
CT>GA 0 0 0 0 1 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 0
CT>GC 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0
CT>GG 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0
CT>TA 1 0 2 0 3 1 0 1 0 0 0 0 2 0 2 8 0 0 0 1 0
CT>TC 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0
CT>TG 0 0 1 0 0 0 0 0 0 0 0 0 0 2 0 0 2 0 0 1 0
GC>AA 2 1 2 4 9 2 4 1 1 0 2 5 0 2 3 3 1 0 0 0 0
GC>AG 0 0 0 0 3 2 2 1 0 0 2 4 1 0 4 2 0 0 1 0 0
GC>AT 0 2 1 0 0 3 0 0 0 0 0 2 1 0 0 0 0 1 0 0 0
GC>CA 0 1 0 0 1 0 0 0 0 1 0 0 0 2 0 1 1 0 0 0 0
GC>CG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
GC>TA 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0
TA>AT 0 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 2 0 0 0 0
TA>CG 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0
TA>CT 0 3 1 0 1 0 1 0 0 0 0 0 2 3 0 0 0 0 0 0 0
TA>GC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TA>GG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
TA>GT 0 0 1 0 0 0 2 0 0 0 0 0 0 0 1 0 0 0 1 0 0
TC>AA 0 2 5 4 19 4 4 0 0 1 3 2 4 14 4 1 1 0 0 1 4
TC>AG 0 0 0 2 0 2 0 0 0 0 0 0 3 1 2 6 0 0 0 0 0
TC>AT 0 1 4 1 7 1 3 0 0 0 4 4 4 1 4 20 0 0 2 3 1
TC>CA 0 1 6 1 5 0 0 0 0 0 1 1 0 4 3 1 0 0 0 0 1
TC>CG 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 1 0
TC>CT 1 0 1 0 1 0 2 0 0 0 0 2 1 2 2 4 1 0 0 0 0
TC>GA 1 0 1 0 5 1 0 0 0 0 2 4 0 1 1 0 0 0 0 0 0
TC>GG 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 2 0 0 0 0 0
TC>GT 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0
TG>AA 0 0 0 0 1 0 0 0 0 0 0 1 0 2 1 0 0 0 0 0 0
TG>AC 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
TG>AT 0 2 1 0 4 2 2 0 0 1 0 2 1 4 2 0 0 0 0 0 2
TG>CA 0 0 2 2 2 3 2 0 1 0 0 1 0 2 0 2 2 0 0 1 2
TG>CC 0 0 1 0 0 0 1 0 1 0 1 0 0 0 0 2 0 1 1 0 1
TG>CT 0 0 5 1 3 5 5 1 1 0 1 4 4 9 1 0 0 2 1 1 2
TG>GA 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
TG>GC 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0
TG>GT 0 0 1 0 1 1 1 0 0 0 0 0 1 2 1 2 0 0 1 0 0
TT>AA 0 1 0 0 3 0 0 0 0 1 0 1 0 5 1 2 0 1 0 0 1
TT>AC 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
TT>AG 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
TT>CA 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0
TT>CC 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0
TT>CG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0
TT>GA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TT>GC 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0
TT>GG 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
97 changes: 97 additions & 0 deletions SigProfilerAssignment/data/tests/txt_input/sample_matrix_SBS.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,97 @@
MutationType SP.Syn.Abst.1 SP.Syn.Abst.2 SP.Syn.Abst.3 SP.Syn.Abst.4 SP.Syn.Abst.5
A[C>A]A 152 117 126 118 186
A[C>A]C 94 81 84 67 121
A[C>A]G 15 11 12 12 18
A[C>A]T 84 66 70 64 104
A[C>G]A 100 92 92 67 132
A[C>G]C 63 56 57 44 83
A[C>G]G 9 4 6 8 9
A[C>G]T 101 86 89 72 129
A[C>T]A 136 87 97 98 142
A[C>T]C 90 67 71 63 103
A[C>T]G 15 12 12 8 16
A[C>T]T 109 73 80 80 118
A[T>A]A 41 30 33 30 47
A[T>A]C 40 35 35 27 50
A[T>A]G 57 47 49 39 70
A[T>A]T 55 38 42 44 63
A[T>C]A 155 98 109 106 157
A[T>C]C 58 42 45 40 65
A[T>C]G 125 76 86 87 123
A[T>C]T 150 100 109 104 158
A[T>G]A 36 25 28 29 42
A[T>G]C 31 19 22 26 35
A[T>G]G 50 36 39 37 57
A[T>G]T 70 39 48 63 75
C[C>A]A 129 113 116 95 169
C[C>A]C 117 115 114 79 163
C[C>A]G 18 14 14 13 21
C[C>A]T 91 78 81 67 118
C[C>G]A 81 84 81 51 115
C[C>G]C 76 67 68 51 97
C[C>G]G 12 8 9 9 13
C[C>G]T 111 104 104 75 149
C[C>T]A 124 90 98 91 143
C[C>T]C 127 103 107 89 155
C[C>T]G 34 16 19 21 27
C[C>T]T 152 120 126 108 183
C[T>A]A 28 32 30 15 41
C[T>A]C 75 78 76 48 107
C[T>A]G 51 55 53 30 73
C[T>A]T 66 61 61 46 88
C[T>C]A 72 50 55 52 80
C[T>C]C 80 70 71 54 102
C[T>C]G 83 57 62 57 89
C[T>C]T 100 81 84 70 121
C[T>G]A 24 21 22 17 31
C[T>G]C 41 35 36 29 52
C[T>G]G 52 49 49 34 69
C[T>G]T 66 45 50 53 75
G[C>A]A 73 47 54 58 81
G[C>A]C 68 56 58 49 85
G[C>A]G 14 9 10 11 15
G[C>A]T 66 53 56 49 82
G[C>G]A 54 55 54 34 76
G[C>G]C 45 41 41 30 58
G[C>G]G 12 11 11 7 15
G[C>G]T 67 66 65 43 92
G[C>T]A 109 85 89 76 128
G[C>T]C 96 71 75 65 108
G[C>T]G 17 5 7 9 9
G[C>T]T 90 63 69 64 100
G[T>A]A 31 31 30 19 42
G[T>A]C 33 33 33 21 46
G[T>A]G 48 50 49 30 68
G[T>A]T 53 54 53 34 75
G[T>C]A 61 49 50 39 71
G[T>C]C 38 29 31 26 44
G[T>C]G 64 52 53 40 75
G[T>C]T 65 51 53 43 76
G[T>G]A 22 20 20 15 29
G[T>G]C 15 12 13 11 18
G[T>G]G 48 48 47 30 66
G[T>G]T 34 29 30 25 44
T[C>A]A 108 66 78 94 121
T[C>A]C 117 92 98 90 145
T[C>A]G 16 10 11 13 17
T[C>A]T 113 71 82 93 125
T[C>G]A 81 68 70 59 103
T[C>G]C 104 96 97 72 139
T[C>G]G 9 5 6 7 9
T[C>G]T 147 121 127 108 185
T[C>T]A 129 65 82 111 128
T[C>T]C 131 85 96 101 143
T[C>T]G 29 11 14 18 19
T[C>T]T 113 64 77 91 116
T[T>A]A 46 35 37 34 55
T[T>A]C 63 53 56 47 81
T[T>A]G 38 33 34 26 48
T[T>A]T 107 77 85 85 127
T[T>C]A 92 75 77 61 110
T[T>C]C 58 46 48 40 69
T[T>C]G 52 37 40 35 57
T[T>C]T 89 70 73 60 104
T[T>G]A 50 39 42 38 61
T[T>G]C 58 40 44 46 67
T[T>G]G 55 43 46 40 67
T[T>G]T 118 74 86 97 130
6 changes: 4 additions & 2 deletions SigProfilerAssignment/decompose_subroutines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,8 @@ def getProcessAvg(samples, genome_build="GRCh37", cosmic_version=3.3, signature_
sigDatabase = pd.read_csv(paths+"/data/Reference_Signatures/GRCh37/COSMIC_v"+str(cosmic_version)+"_ID_GRCh37.txt", sep="\t", index_col=0)
signames = sigDatabase.columns
connected_sigs=False
# indel signatures have no re-normalization so "GRCh37" is used
genome_build="GRCh37"

elif samples.shape[0]==48:
if cosmic_version < 3.3:
Expand All @@ -83,7 +85,7 @@ def getProcessAvg(samples, genome_build="GRCh37", cosmic_version=3.3, signature_
sigDatabase.index=sigDatabase.index.astype(str)
signames=sigDatabase.columns
connected_sigs=False
return sigDatabase,signames,connected_sigs
return sigDatabase,signames,connected_sigs,genome_build

if signature_database != None:#pd.core.frame.DataFrame:
print("################## USING CUSTOM SIGNATURE DATBASE ##################")
Expand Down Expand Up @@ -217,7 +219,7 @@ def signature_decomposition(signatures, mtype, directory, genome_build="GRCh37",


if signature_database==None:
sigDatabase,signames,connected_sigs = getProcessAvg(signatures, genome_build=genome_build, cosmic_version=cosmic_version, exome=exome)
sigDatabase,signames,connected_sigs,genome_build = getProcessAvg(signatures, genome_build=genome_build, cosmic_version=cosmic_version, exome=exome)
#processAvg = processAvg.set_index('Type').rename_axis('MutationType')
else:
try:
Expand Down
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