Skip to content

Commit 327fb93

Browse files
mdbarnesUCSDmdbarnesUCSD
authored
Merge pull request #110 from AlexandrovLab/i108
I108
2 parents 6c6b61b + d99070d commit 327fb93

17 files changed

+13964
-7152
lines changed

‎README.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@ genInstall.install('GRCh37')
3636
```
3737
## <a name="running"></a> Running
3838

39-
Assignment of known mutational signatures to individual samples is performed using the `cosmic_fit` function. Input samples are provided using the `samples` parameter in the form of mutation calling files (VCFs, MAFs, or simple text files), segmentation files or mutational matrices. COSMIC mutational signatures v3.3 are used as the default reference signatures, although previous COSMIC versions and custom signature databases are also supported using the `cosmic_version` and `signature_database` parameters. Results will be found in the folder specified in the `output` parameter.
39+
Assignment of known mutational signatures to individual samples is performed using the `cosmic_fit` function. Input samples are provided using the `samples` parameter in the form of mutation calling files (VCFs, MAFs, or simple text files), segmentation files or mutational matrices. COSMIC mutational signatures v3.4 are used as the default reference signatures, although previous COSMIC versions and custom signature databases are also supported using the `cosmic_version` and `signature_database` parameters. Results will be found in the folder specified in the `output` parameter.
4040

4141
```python
4242
from SigProfilerAssignment import Analyzer as Analyze

‎SigProfilerAssignment/Analyzer.py‎

Lines changed: 148 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,152 @@
11
from SigProfilerAssignment import decomposition as decomp
22

3-
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=3.4, 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, export_probabilities_per_mutation=False):
4-
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, export_probabilities_per_mutation=export_probabilities_per_mutation)
53

6-
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=3.4, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exome=False,input_type='matrix',context_type="96",export_probabilities=True, export_probabilities_per_mutation=False):
7-
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,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation)
4+
def decompose_fit(
5+
samples,
6+
output,
7+
signatures=None,
8+
signature_database=None,
9+
nnls_add_penalty=0.05,
10+
nnls_remove_penalty=0.01,
11+
initial_remove_penalty=0.05,
12+
genome_build="GRCh37",
13+
cosmic_version=3.4,
14+
make_plots=True,
15+
collapse_to_SBS96=True,
16+
connected_sigs=True,
17+
verbose=False,
18+
devopts=None,
19+
new_signature_thresh_hold=0.8,
20+
exclude_signature_subgroups=None,
21+
exome=False,
22+
input_type="matrix",
23+
context_type="96",
24+
export_probabilities=True,
25+
export_probabilities_per_mutation=False,
26+
):
27+
decomp.spa_analyze(
28+
samples=samples,
29+
output=output,
30+
signatures=signatures,
31+
signature_database=signature_database,
32+
nnls_add_penalty=nnls_add_penalty,
33+
nnls_remove_penalty=nnls_remove_penalty,
34+
initial_remove_penalty=initial_remove_penalty,
35+
genome_build=genome_build,
36+
cosmic_version=cosmic_version,
37+
make_plots=make_plots,
38+
collapse_to_SBS96=collapse_to_SBS96,
39+
connected_sigs=connected_sigs,
40+
verbose=verbose,
41+
decompose_fit_option=True,
42+
denovo_refit_option=False,
43+
cosmic_fit_option=False,
44+
devopts=devopts,
45+
new_signature_thresh_hold=new_signature_thresh_hold,
46+
exclude_signature_subgroups=exclude_signature_subgroups,
47+
exome=exome,
48+
input_type=input_type,
49+
context_type=context_type,
50+
export_probabilities=export_probabilities,
51+
export_probabilities_per_mutation=export_probabilities_per_mutation,
52+
)
853

9-
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=3.4, 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, export_probabilities_per_mutation=False, sample_reconstruction_plots=False):
10-
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, export_probabilities_per_mutation=export_probabilities_per_mutation, sample_reconstruction_plots=sample_reconstruction_plots)
54+
55+
def denovo_fit(
56+
samples,
57+
output,
58+
signatures=None,
59+
signature_database=None,
60+
nnls_add_penalty=0.05,
61+
nnls_remove_penalty=0.01,
62+
initial_remove_penalty=0.05,
63+
genome_build="GRCh37",
64+
cosmic_version=3.4,
65+
make_plots=True,
66+
collapse_to_SBS96=True,
67+
connected_sigs=True,
68+
verbose=False,
69+
devopts=None,
70+
new_signature_thresh_hold=0.8,
71+
exome=False,
72+
input_type="matrix",
73+
context_type="96",
74+
export_probabilities=True,
75+
export_probabilities_per_mutation=False,
76+
):
77+
decomp.spa_analyze(
78+
samples=samples,
79+
output=output,
80+
signatures=signatures,
81+
signature_database=signature_database,
82+
nnls_add_penalty=nnls_add_penalty,
83+
nnls_remove_penalty=nnls_remove_penalty,
84+
initial_remove_penalty=initial_remove_penalty,
85+
genome_build=genome_build,
86+
cosmic_version=cosmic_version,
87+
new_signature_thresh_hold=new_signature_thresh_hold,
88+
make_plots=make_plots,
89+
collapse_to_SBS96=collapse_to_SBS96,
90+
connected_sigs=connected_sigs,
91+
verbose=verbose,
92+
decompose_fit_option=False,
93+
denovo_refit_option=True,
94+
cosmic_fit_option=False,
95+
devopts=devopts,
96+
exome=exome,
97+
input_type=input_type,
98+
context_type=context_type,
99+
export_probabilities=export_probabilities,
100+
export_probabilities_per_mutation=export_probabilities_per_mutation,
101+
)
102+
103+
104+
def cosmic_fit(
105+
samples,
106+
output,
107+
signatures=None,
108+
signature_database=None,
109+
nnls_add_penalty=0.05,
110+
nnls_remove_penalty=0.01,
111+
initial_remove_penalty=0.05,
112+
genome_build="GRCh37",
113+
cosmic_version=3.4,
114+
make_plots=True,
115+
collapse_to_SBS96=True,
116+
connected_sigs=True,
117+
verbose=False,
118+
devopts=None,
119+
exclude_signature_subgroups=None,
120+
exome=False,
121+
input_type="matrix",
122+
context_type="96",
123+
export_probabilities=True,
124+
export_probabilities_per_mutation=False,
125+
sample_reconstruction_plots=False,
126+
):
127+
decomp.spa_analyze(
128+
samples=samples,
129+
output=output,
130+
signatures=signatures,
131+
signature_database=signature_database,
132+
nnls_add_penalty=nnls_add_penalty,
133+
nnls_remove_penalty=nnls_remove_penalty,
134+
initial_remove_penalty=initial_remove_penalty,
135+
genome_build=genome_build,
136+
cosmic_version=cosmic_version,
137+
make_plots=make_plots,
138+
collapse_to_SBS96=collapse_to_SBS96,
139+
connected_sigs=connected_sigs,
140+
verbose=verbose,
141+
decompose_fit_option=False,
142+
denovo_refit_option=False,
143+
cosmic_fit_option=True,
144+
devopts=devopts,
145+
exclude_signature_subgroups=exclude_signature_subgroups,
146+
exome=exome,
147+
input_type=input_type,
148+
context_type=context_type,
149+
export_probabilities=export_probabilities,
150+
export_probabilities_per_mutation=export_probabilities_per_mutation,
151+
sample_reconstruction_plots=sample_reconstruction_plots,
152+
)

0 commit comments

Comments
 (0)