Merge pull request #20 from AlexandrovLab/spmods

performance upgrades

.gitignore

@@ -7,6 +7,8 @@
 # Python egg metadata, regenerated from source files by setuptools.
 /*.egg-info
 
+sigProfilerPlotting/templates/**
+
 # Hidden files and directories
 *.DS_Store
 

.travis.yml

@@ -1,11 +1,11 @@
 language: python
 
 python:
-  - '3.6'
+  - "3.9.13"
 
 install:
   - pip install -q matplotlib
-  - pip install .
+  - pip install . -v
 
 script: python3 plot_example.py
 

build/lib/sigProfilerPlotting/version.py

@@ -1,6 +1,6 @@
 
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
-short_version = '1.2.2'
-version = '1.2.2'
+short_version = '1.2.3'
+version = '1.2.3'
 
 

input/examples/samples/test288.all

@@ -0,0 +1,289 @@
+MutationType	Sample 1	Sample 2	Sample 3	Sample 4	Sample 5	Sample 6
+T:A[C>A]A	15	22	10	8	15	19
+T:A[C>A]C	13	12	6	3	9	22
+T:A[C>A]G	4	3	3	0	2	8
+T:A[C>A]T	12	8	8	5	19	4
+T:A[C>G]A	13	13	6	7	5	7
+T:A[C>G]C	8	9	3	4	4	3
+T:A[C>G]G	0	2	3	0	2	1
+T:A[C>G]T	6	9	5	5	9	8
+T:A[C>T]A	32	12	23	10	17	18
+T:A[C>T]C	10	11	12	10	14	14
+T:A[C>T]G	26	15	15	13	24	16
+T:A[C>T]T	22	11	14	14	23	11
+T:A[T>A]A	11	9	5	8	10	6
+T:A[T>A]C	7	3	4	2	2	9
+T:A[T>A]G	6	5	6	1	7	7
+T:A[T>A]T	4	6	9	7	29	11
+T:A[T>C]A	40	55	22	22	38	46
+T:A[T>C]C	17	29	5	3	19	17
+T:A[T>C]G	24	38	21	10	43	46
+T:A[T>C]T	26	42	14	26	24	31
+T:A[T>G]A	8	5	5	1	3	4
+T:A[T>G]C	5	2	6	2	3	3
+T:A[T>G]G	6	1	3	4	6	3
+T:A[T>G]T	7	4	8	9	11	8
+T:C[C>A]A	17	24	16	8	17	14
+T:C[C>A]C	11	21	10	3	8	20
+T:C[C>A]G	3	2	0	0	1	5
+T:C[C>A]T	8	15	11	6	14	12
+T:C[C>G]A	9	8	3	1	4	8
+T:C[C>G]C	11	7	4	2	10	8
+T:C[C>G]G	0	0	3	1	1	1
+T:C[C>G]T	7	8	2	5	10	5
+T:C[C>T]A	16	12	12	7	21	6
+T:C[C>T]C	18	14	15	5	18	16
+T:C[C>T]G	12	9	9	6	18	16
+T:C[C>T]T	14	20	15	10	19	10
+T:C[T>A]A	2	4	6	3	6	6
+T:C[T>A]C	2	9	6	1	14	13
+T:C[T>A]G	5	7	6	4	11	11
+T:C[T>A]T	1	6	5	3	13	7
+T:C[T>C]A	7	17	9	6	18	17
+T:C[T>C]C	12	16	6	5	14	20
+T:C[T>C]G	12	16	6	8	16	11
+T:C[T>C]T	18	21	9	13	25	16
+T:C[T>G]A	0	1	1	1	5	5
+T:C[T>G]C	1	1	5	2	8	1
+T:C[T>G]G	4	3	2	2	8	5
+T:C[T>G]T	7	3	4	7	13	8
+T:G[C>A]A	12	14	12	4	9	13
+T:G[C>A]C	4	9	7	6	3	9
+T:G[C>A]G	3	1	2	2	1	1
+T:G[C>A]T	3	6	7	4	5	9
+T:G[C>G]A	3	5	2	1	2	6
+T:G[C>G]C	7	2	4	3	1	5
+T:G[C>G]G	1	2	1	1	2	1
+T:G[C>G]T	2	6	3	2	5	6
+T:G[C>T]A	22	21	8	9	15	16
+T:G[C>T]C	20	14	13	3	10	10
+T:G[C>T]G	15	6	10	8	19	15
+T:G[C>T]T	11	11	11	8	23	16
+T:G[T>A]A	0	1	3	2	8	3
+T:G[T>A]C	2	2	0	2	6	2
+T:G[T>A]G	1	2	3	1	6	2
+T:G[T>A]T	1	10	5	1	5	0
+T:G[T>C]A	14	25	5	10	12	16
+T:G[T>C]C	11	16	1	5	13	9
+T:G[T>C]G	5	14	2	4	12	9
+T:G[T>C]T	12	22	6	8	13	6
+T:G[T>G]A	0	1	0	2	2	2
+T:G[T>G]C	0	0	0	2	0	2
+T:G[T>G]G	0	2	1	1	1	3
+T:G[T>G]T	0	0	2	2	3	3
+T:T[C>A]A	14	16	11	10	17	14
+T:T[C>A]C	14	10	14	8	15	19
+T:T[C>A]G	4	2	0	1	1	2
+T:T[C>A]T	10	13	17	11	13	16
+T:T[C>G]A	4	8	4	6	7	7
+T:T[C>G]C	6	9	6	9	7	8
+T:T[C>G]G	1	0	0	2	0	1
+T:T[C>G]T	10	8	10	7	13	19
+T:T[C>T]A	9	20	12	16	17	24
+T:T[C>T]C	11	21	11	21	9	26
+T:T[C>T]G	14	5	6	7	11	13
+T:T[C>T]T	13	16	15	7	17	17
+T:T[T>A]A	2	6	6	10	8	4
+T:T[T>A]C	5	15	4	2	11	5
+T:T[T>A]G	4	4	1	3	6	8
+T:T[T>A]T	7	8	7	2	13	8
+T:T[T>C]A	35	41	2	9	10	40
+T:T[T>C]C	13	25	3	6	11	9
+T:T[T>C]G	9	14	1	1	13	14
+T:T[T>C]T	23	29	8	10	12	29
+T:T[T>G]A	4	4	4	7	6	6
+T:T[T>G]C	7	4	4	3	3	3
+T:T[T>G]G	2	7	8	1	2	9
+T:T[T>G]T	12	5	11	6	11	9
+U:A[C>A]A	21	15	17	5	18	19
+U:A[C>A]C	13	7	7	2	14	10
+U:A[C>A]G	0	0	1	0	1	1
+U:A[C>A]T	8	6	4	4	9	11
+U:A[C>G]A	3	8	6	3	7	12
+U:A[C>G]C	5	4	5	0	3	6
+U:A[C>G]G	1	0	3	0	1	0
+U:A[C>G]T	7	9	5	3	10	12
+U:A[C>T]A	19	15	21	7	15	11
+U:A[C>T]C	7	10	9	8	5	6
+U:A[C>T]G	27	8	7	11	18	12
+U:A[C>T]T	13	11	13	6	11	15
+U:A[T>A]A	8	9	4	6	11	9
+U:A[T>A]C	2	3	1	2	10	5
+U:A[T>A]G	8	6	8	5	13	2
+U:A[T>A]T	12	9	11	8	41	9
+U:A[T>C]A	19	25	10	19	35	22
+U:A[T>C]C	8	15	8	6	16	14
+U:A[T>C]G	16	13	9	20	42	30
+U:A[T>C]T	14	21	12	9	37	21
+U:A[T>G]A	3	2	3	5	8	4
+U:A[T>G]C	3	3	2	5	8	6
+U:A[T>G]G	3	7	2	2	13	4
+U:A[T>G]T	10	7	6	10	17	6
+U:C[C>A]A	16	30	8	5	15	17
+U:C[C>A]C	9	13	11	3	13	18
+U:C[C>A]G	3	0	3	2	2	3
+U:C[C>A]T	9	13	12	6	21	14
+U:C[C>G]A	1	9	5	4	2	5
+U:C[C>G]C	7	6	8	3	6	6
+U:C[C>G]G	1	1	1	1	3	4
+U:C[C>G]T	9	7	5	5	10	8
+U:C[C>T]A	14	26	9	5	6	17
+U:C[C>T]C	9	11	12	6	19	14
+U:C[C>T]G	7	2	8	12	7	11
+U:C[C>T]T	11	20	5	14	15	14
+U:C[T>A]A	7	2	4	9	10	8
+U:C[T>A]C	6	8	7	4	12	8
+U:C[T>A]G	15	8	8	11	34	12
+U:C[T>A]T	7	6	10	5	18	11
+U:C[T>C]A	6	7	15	12	21	9
+U:C[T>C]C	4	8	7	8	17	7
+U:C[T>C]G	6	8	10	15	30	18
+U:C[T>C]T	10	9	6	10	26	10
+U:C[T>G]A	4	1	1	3	2	2
+U:C[T>G]C	3	3	4	4	8	9
+U:C[T>G]G	1	1	4	5	4	5
+U:C[T>G]T	5	12	6	7	13	8
+U:G[C>A]A	11	12	7	5	12	14
+U:G[C>A]C	5	8	6	6	4	5
+U:G[C>A]G	1	3	3	0	0	4
+U:G[C>A]T	8	8	5	2	5	3
+U:G[C>G]A	2	3	2	2	4	3
+U:G[C>G]C	3	2	1	4	5	2
+U:G[C>G]G	0	1	0	0	4	0
+U:G[C>G]T	6	4	4	3	4	7
+U:G[C>T]A	14	13	11	7	21	20
+U:G[C>T]C	10	19	5	9	14	12
+U:G[C>T]G	14	8	1	14	12	9
+U:G[C>T]T	9	11	9	7	12	8
+U:G[T>A]A	2	2	2	1	5	5
+U:G[T>A]C	1	5	2	1	8	4
+U:G[T>A]G	4	5	6	3	10	5
+U:G[T>A]T	5	5	6	4	7	6
+U:G[T>C]A	20	14	8	12	11	15
+U:G[T>C]C	7	4	1	12	9	10
+U:G[T>C]G	4	11	6	12	20	12
+U:G[T>C]T	11	15	3	14	13	8
+U:G[T>G]A	4	1	0	1	1	1
+U:G[T>G]C	3	0	1	2	0	1
+U:G[T>G]G	5	3	1	0	3	3
+U:G[T>G]T	4	4	2	3	0	4
+U:T[C>A]A	10	13	15	7	24	18
+U:T[C>A]C	10	14	9	9	12	17
+U:T[C>A]G	4	2	3	2	3	2
+U:T[C>A]T	16	19	11	15	19	11
+U:T[C>G]A	11	3	3	6	6	11
+U:T[C>G]C	3	4	4	5	9	10
+U:T[C>G]G	3	2	1	0	2	3
+U:T[C>G]T	13	14	9	12	20	17
+U:T[C>T]A	16	19	21	13	20	34
+U:T[C>T]C	23	19	15	9	17	25
+U:T[C>T]G	9	12	8	4	12	5
+U:T[C>T]T	12	10	8	9	12	21
+U:T[T>A]A	4	8	11	10	11	16
+U:T[T>A]C	1	8	5	5	9	5
+U:T[T>A]G	3	4	3	8	12	6
+U:T[T>A]T	13	13	8	4	23	23
+U:T[T>C]A	12	18	9	7	14	26
+U:T[T>C]C	8	13	4	4	9	8
+U:T[T>C]G	12	12	6	3	15	7
+U:T[T>C]T	13	12	13	6	25	18
+U:T[T>G]A	8	4	2	7	6	5
+U:T[T>G]C	7	6	5	3	14	5
+U:T[T>G]G	4	5	2	2	7	7
+U:T[T>G]T	16	20	17	19	19	15
+N:A[C>A]A	73	105	64	40	45	110
+N:A[C>A]C	30	43	16	17	17	54
+N:A[C>A]G	10	10	6	2	6	10
+N:A[C>A]T	46	48	37	17	27	46
+N:A[C>G]A	43	36	20	17	21	32
+N:A[C>G]C	10	14	16	8	10	17
+N:A[C>G]G	4	4	1	4	4	0
+N:A[C>G]T	25	24	21	12	22	23
+N:A[C>T]A	48	54	36	25	58	39
+N:A[C>T]C	31	38	24	22	30	26
+N:A[C>T]G	83	51	36	36	74	56
+N:A[C>T]T	40	43	32	21	50	49
+N:A[T>A]A	27	20	18	11	36	49
+N:A[T>A]C	18	13	15	6	13	26
+N:A[T>A]G	23	24	16	8	31	29
+N:A[T>A]T	12	22	28	21	62	43
+N:A[T>C]A	90	134	45	53	63	116
+N:A[T>C]C	44	80	11	16	32	38
+N:A[T>C]G	62	85	28	41	75	70
+N:A[T>C]T	74	105	39	38	55	85
+N:A[T>G]A	15	11	10	9	14	17
+N:A[T>G]C	6	8	7	5	12	13
+N:A[T>G]G	9	16	11	8	19	16
+N:A[T>G]T	10	17	15	7	19	18
+N:C[C>A]A	80	102	40	19	41	86
+N:C[C>A]C	38	63	24	16	36	52
+N:C[C>A]G	4	6	13	4	9	8
+N:C[C>A]T	55	56	36	19	34	47
+N:C[C>G]A	13	18	17	6	10	20
+N:C[C>G]C	10	20	12	7	23	18
+N:C[C>G]G	4	2	4	2	2	5
+N:C[C>G]T	24	27	18	16	23	36
+N:C[C>T]A	48	51	28	18	39	44
+N:C[C>T]C	41	54	33	20	55	45
+N:C[C>T]G	36	33	23	27	30	34
+N:C[C>T]T	45	58	37	32	47	62
+N:C[T>A]A	17	14	13	8	28	26
+N:C[T>A]C	16	39	14	9	27	24
+N:C[T>A]G	20	21	17	13	39	35
+N:C[T>A]T	17	21	23	10	34	33
+N:C[T>C]A	23	38	26	31	46	50
+N:C[T>C]C	28	60	15	15	11	48
+N:C[T>C]G	25	53	13	27	40	35
+N:C[T>C]T	36	67	18	29	27	56
+N:C[T>G]A	6	1	4	7	7	9
+N:C[T>G]C	11	10	5	5	9	12
+N:C[T>G]G	11	11	8	11	10	14
+N:C[T>G]T	10	10	7	19	12	22
+N:G[C>A]A	35	58	31	24	20	43
+N:G[C>A]C	19	35	24	6	14	32
+N:G[C>A]G	10	6	5	4	4	9
+N:G[C>A]T	24	37	21	16	12	35
+N:G[C>G]A	8	15	14	7	7	12
+N:G[C>G]C	11	9	8	7	17	17
+N:G[C>G]G	5	1	2	1	0	1
+N:G[C>G]T	7	12	9	8	10	15
+N:G[C>T]A	38	46	34	23	33	55
+N:G[C>T]C	30	37	31	18	28	47
+N:G[C>T]G	42	32	33	28	61	42
+N:G[C>T]T	36	55	47	27	42	55
+N:G[T>A]A	13	7	8	3	13	11
+N:G[T>A]C	11	18	7	3	6	9
+N:G[T>A]G	7	14	4	5	15	13
+N:G[T>A]T	14	11	17	9	19	17
+N:G[T>C]A	40	83	15	24	26	69
+N:G[T>C]C	26	46	7	14	18	32
+N:G[T>C]G	31	44	12	14	17	29
+N:G[T>C]T	35	51	23	28	29	48
+N:G[T>G]A	5	1	5	1	4	5
+N:G[T>G]C	1	4	4	0	5	5
+N:G[T>G]G	8	6	3	4	11	8
+N:G[T>G]T	7	7	5	7	5	5
+N:T[C>A]A	36	52	40	29	28	59
+N:T[C>A]C	43	59	40	24	21	76
+N:T[C>A]G	3	6	7	3	2	15
+N:T[C>A]T	34	55	38	39	34	75
+N:T[C>G]A	17	23	14	15	17	23
+N:T[C>G]C	20	28	13	10	26	38
+N:T[C>G]G	1	4	1	0	4	5
+N:T[C>G]T	27	40	31	28	41	54
+N:T[C>T]A	46	59	44	31	45	64
+N:T[C>T]C	56	71	36	22	46	66
+N:T[C>T]G	18	14	22	14	31	23
+N:T[C>T]T	35	39	54	42	47	52
+N:T[T>A]A	22	20	23	24	29	32
+N:T[T>A]C	22	32	20	4	27	33
+N:T[T>A]G	16	20	11	9	20	21
+N:T[T>A]T	29	29	30	23	44	36
+N:T[T>C]A	74	113	15	27	45	61
+N:T[T>C]C	46	76	9	19	22	35
+N:T[T>C]G	33	70	11	11	25	56
+N:T[T>C]T	60	99	13	30	39	78
+N:T[T>G]A	17	13	7	14	12	11
+N:T[T>G]C	15	12	15	8	24	23
+N:T[T>G]G	9	10	7	6	14	23
+N:T[T>G]T	32	28	22	23	36	41

plot_example.py

@@ -16,4 +16,4 @@
 sigPlt.plotSV(matrix_path + "breast_cancer_samples_example.RS32.all", output_path, "BRCA_example", "pdf", percentage=False, aggregate=False) #plotting of SV counts
 
 #sigPlt.plotDBS(matrix_path + "breast_cancer_samples_example.DBS78.all", output_path, "BRCA_example", "78")
-#sigPlt.plotID(matrix_path + "breast_cancer_samples_example.ID94.all", output_path,  "BRCA_example", "94")
+# sigPlt.plotID(matrix_path + "breast_cancer_samples_example.ID94.all", output_path,  "BRCA_example", "94")

setup.py

@@ -12,7 +12,7 @@ def readme():
 	with open('README.rst') as f:
 		return(f.read())
 
-VERSION = '1.2.2'
+VERSION = '1.2.3'
 
 def write_version_py(filename='sigProfilerPlotting/version.py'):
     # Copied from numpy setup.py
@@ -53,13 +53,23 @@ def run(self):
             file_names = ["Times New Roman.ttf", "Arial.ttf", "Courier New.ttf", 
             			  "Courier New Bold.ttf", "Arial Bold.ttf", "Times New Roman Bold.ttf"]
             for file in file_names:
-            	old_path = os.path.join(cp_ttf_dir, "fonts/" + file)
-            	new_path = os.path.join(mpl_ttf_dir, file)
-            	shutil.copyfile(old_path, new_path)
+                old_path = os.path.join(cp_ttf_dir, "fonts/" + file)
+                new_path = os.path.join(mpl_ttf_dir, file)
+                shutil.copyfile(old_path, new_path)
             matplotlib.font_manager._rebuild()
 
         except:
             warnings.warn("WARNING: An issue occured while installing the fonts.")
+        #install figure templates
+        try:
+            import sigProfilerPlotting as sigPlt
+            sigPlt.install_plot_templates('SBS96')
+            sigPlt.install_plot_templates('SBS288')
+            sigPlt.install_plot_templates('DBS78')
+            sigPlt.install_plot_templates('ID83')
+            os.system("echo 'installed figure templates' ")
+        except:
+            os.system("echo 'Failed to install templates' ")
 
 
 
@@ -72,9 +82,10 @@ def run(self):
 		license='UCSD',
 		packages=['sigProfilerPlotting'],
 		install_requires =[
-			"matplotlib>=3.3.0,<=3.4.3", "pandas", "seaborn"],
+			"matplotlib>=3.3.0,<=3.4.3", "pandas", "seaborn","sklearn"],
         package_data={'':['fonts/*.ttf']},
 		include_package_data=True,
 	    #Specify the custom install class
 	    cmdclass={'install' : move_ttf},
 		zip_safe=False)
+