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test.py
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test.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
12/2/2021
@author: rvangara
"""
import SigProfilerAssignment as spa
from SigProfilerAssignment import Analyzer as Analyze
from SigProfilerAssignment.DecompositionPlots import PlotDecomposition as sp
from pypdf import PdfWriter, PdfReader
import numpy as np
import pandas as pd
import time
import os
DIR_INPUT = spa.__path__[0] + "/data/tests/"
OUTPUT_MATRIX = "TestOutput/output_matrix_example/"
OUTPUT_VCF = "TestOutput/output_vcf_example/"
SIGNATURES_MATRIX_SBS = os.path.join(DIR_INPUT, "txt_input/SBS96_S3_Signatures.txt")
SIGNATURES_MATRIX_DBS = os.path.join(DIR_INPUT, "txt_input/DBS78_S3_Signatures.txt")
SIGNATURES_MATRIX_ID = os.path.join(DIR_INPUT, "txt_input/ID83_S3_Signatures.txt")
SIGNATURES_MATRIX_CNV = os.path.join(DIR_INPUT, "txt_input/CNV48_S3_Signatures.txt")
SIGNATURES_MATRIX_SV = os.path.join(DIR_INPUT, "txt_input/SV32_S3_Signatures.txt")
SAMPLE_MATRIX_SBS = os.path.join(DIR_INPUT, "txt_input/sample_matrix_SBS.txt")
SAMPLE_MATRIX_DBS = os.path.join(DIR_INPUT, "txt_input/sample_matrix_DBS.txt")
SAMPLE_MATRIX_ID = os.path.join(DIR_INPUT, "txt_input/sample_matrix_ID.txt")
SAMPLE_MATRIX_CNV = os.path.join(DIR_INPUT, "txt_input/sample_matrix_CNV48.txt")
SAMPLE_MATRIX_SV = os.path.join(DIR_INPUT, "txt_input/sample_matrix_SV32.txt")
SAMPLES_VCF = os.path.join(DIR_INPUT, "vcf_input/")
exclude_signature_subgroups = None
########### SBS Tests ###########
def cosmic_fit_SBS_matrix_test():
Analyze.cosmic_fit(
SAMPLE_MATRIX_SBS,
os.path.join(OUTPUT_MATRIX, "cosmic_fit_SBS_matrix_test"),
signatures=None,
signature_database=None,
genome_build="GRCh37",
verbose=False,
collapse_to_SBS96=True,
exclude_signature_subgroups=exclude_signature_subgroups,
sample_reconstruction_plots="both",
cosmic_version=3.4,
)
def denovo_fit_SBS_matrix_test():
Analyze.denovo_fit(
SAMPLE_MATRIX_SBS,
os.path.join(OUTPUT_MATRIX, "denovo_fit_SBS_matrix_test"),
signatures=SIGNATURES_MATRIX_SBS,
signature_database=None,
genome_build="GRCh37",
verbose=False,
)
def decompose_fit_SBS_matrix_test():
Analyze.decompose_fit(
SAMPLE_MATRIX_SBS,
os.path.join(OUTPUT_MATRIX, "decompose_fit_SBS_matrix_test"),
signatures=SIGNATURES_MATRIX_SBS,
signature_database=None,
genome_build="GRCh37",
verbose=False,
new_signature_thresh_hold=0.8,
exclude_signature_subgroups=exclude_signature_subgroups,
)
########### DBS Tests ###########
def cosmic_fit_DBS_matrix_test():
Analyze.cosmic_fit(
SAMPLE_MATRIX_DBS,
os.path.join(OUTPUT_MATRIX, "cosmic_fit_DBS_matrix_test"),
signatures=None,
signature_database=None,
genome_build="GRCh37",
verbose=False,
collapse_to_SBS96=False,
exclude_signature_subgroups=exclude_signature_subgroups,
sample_reconstruction_plots=True,
cosmic_version=3.4,
)
def denovo_fit_DBS_matrix_test():
Analyze.denovo_fit(
SAMPLE_MATRIX_DBS,
os.path.join(OUTPUT_MATRIX, "denovo_fit_DBS_matrix_test"),
signatures=SIGNATURES_MATRIX_DBS,
signature_database=None,
genome_build="GRCh37",
verbose=False,
)
def decompose_fit_DBS_matrix_test():
Analyze.decompose_fit(
SAMPLE_MATRIX_DBS,
os.path.join(OUTPUT_MATRIX, "decompose_fit_DBS_matrix_test"),
signatures=SIGNATURES_MATRIX_DBS,
signature_database=None,
genome_build="GRCh37",
verbose=False,
new_signature_thresh_hold=0.8,
exclude_signature_subgroups=exclude_signature_subgroups,
)
########### ID Tests ###########
def decompose_fit_ID_matrix_test():
Analyze.decompose_fit(
SAMPLE_MATRIX_ID,
os.path.join(OUTPUT_MATRIX, "decompose_fit_ID_matrix_test"),
signatures=SIGNATURES_MATRIX_ID,
signature_database=None,
genome_build="GRCh37",
verbose=False,
new_signature_thresh_hold=0.8,
exclude_signature_subgroups=exclude_signature_subgroups,
)
def cosmic_fit_ID_matrix_test():
Analyze.cosmic_fit(
SAMPLE_MATRIX_ID,
os.path.join(OUTPUT_MATRIX, "cosmic_fit_ID_matrix_test"),
signatures=None,
signature_database=None,
genome_build="GRCh37",
verbose=False,
collapse_to_SBS96=False,
exclude_signature_subgroups=exclude_signature_subgroups,
sample_reconstruction_plots=True,
cosmic_version=3.4,
)
def denovo_fit_ID_matrix_test():
Analyze.denovo_fit(
SAMPLE_MATRIX_ID,
os.path.join(OUTPUT_MATRIX, "denovo_fit_ID_matrix_test"),
signatures=SIGNATURES_MATRIX_ID,
signature_database=None,
genome_build="GRCh37",
verbose=False,
)
########### SV Tests ###########
def decompose_fit_SV_matrix_test():
Analyze.decompose_fit(
SAMPLE_MATRIX_SV,
os.path.join(OUTPUT_MATRIX, "decompose_fit_SV_matrix_test"),
signatures=SIGNATURES_MATRIX_SV,
signature_database=None,
genome_build="GRCh37",
verbose=False,
new_signature_thresh_hold=0.8,
exclude_signature_subgroups=exclude_signature_subgroups,
)
def cosmic_fit_SV_matrix_test():
Analyze.cosmic_fit(
SAMPLE_MATRIX_SV,
os.path.join(OUTPUT_MATRIX, "cosmic_fit_SV_matrix_test"),
signatures=None,
signature_database=None,
genome_build="GRCh38",
verbose=False,
collapse_to_SBS96=False,
exclude_signature_subgroups=exclude_signature_subgroups,
sample_reconstruction_plots=True,
cosmic_version=3.4,
)
def denovo_fit_SV_matrix_test():
Analyze.denovo_fit(
SAMPLE_MATRIX_SV,
os.path.join(OUTPUT_MATRIX, "denovo_fit_SV_matrix_test"),
signatures=SIGNATURES_MATRIX_SV,
signature_database=None,
genome_build="GRCh37",
verbose=False,
)
########### CNV Tests ###########
def decompose_fit_CNV_matrix_test():
Analyze.decompose_fit(
SAMPLE_MATRIX_CNV,
os.path.join(OUTPUT_MATRIX, "decompose_fit_CNV_matrix_test"),
signatures=SIGNATURES_MATRIX_CNV,
signature_database=None,
genome_build="GRCh37",
verbose=False,
new_signature_thresh_hold=0.8,
exclude_signature_subgroups=exclude_signature_subgroups,
)
def cosmic_fit_CNV_matrix_test():
Analyze.cosmic_fit(
SAMPLE_MATRIX_CNV,
os.path.join(OUTPUT_MATRIX, "cosmic_fit_CNV_matrix_test"),
signatures=None,
signature_database=None,
genome_build="GRCh37",
verbose=False,
collapse_to_SBS96=False,
exclude_signature_subgroups=exclude_signature_subgroups,
sample_reconstruction_plots=True,
cosmic_version=3.4,
)
def denovo_fit_CNV_matrix_test():
Analyze.denovo_fit(
SAMPLE_MATRIX_CNV,
os.path.join(OUTPUT_MATRIX, "denovo_fit_CNV_matrix_test"),
signatures=SIGNATURES_MATRIX_CNV,
signature_database=None,
genome_build="GRCh37",
verbose=False,
)
########### VCF Tests ###########
def cosmic_fit_vcf_test():
Analyze.cosmic_fit(
SAMPLES_VCF,
OUTPUT_VCF,
input_type="vcf",
signatures=None,
signature_database=None,
genome_build="GRCh37",
verbose=False,
collapse_to_SBS96=True,
exclude_signature_subgroups=exclude_signature_subgroups,
make_plots=True,
)
def decompose_fit_vcf_test():
Analyze.decompose_fit(
SAMPLES_VCF,
OUTPUT_VCF,
input_type="vcf",
signatures=SIGNATURES_MATRIX_SBS,
signature_database=None,
genome_build="GRCh37",
verbose=False,
new_signature_thresh_hold=0.8,
exclude_signature_subgroups=exclude_signature_subgroups,
make_plots=True,
)
def denovo_fit_vcf_test():
Analyze.denovo_fit(
SAMPLES_VCF,
OUTPUT_VCF,
signatures=SIGNATURES_MATRIX_SBS,
signature_database=None,
genome_build="GRCh37",
verbose=False,
make_plots=True,
input_type="vcf",
)
################################################
# Decomposition Plot Tests #
################################################
def gen_SBS96():
np.random.seed(1234567)
s = time.time()
merger = PdfWriter()
file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS96.txt"
file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/Decomposed_Solution_Signatures_SBS96.txt"
denovo_mtx = pd.read_csv(file1, sep="\t")
basis_mtx = pd.read_csv(file2, sep="\t")
output_path = "TestOutput/Results/"
project = "test_run"
mtype = "96"
denovo_name = "SBS96A"
basis_names = ["SBS1", "SBS3", "SBS5", "SBS13", "SBS50", "SBS2"]
weights = ["0.94%", "48.72%", "28.44%", "8.42%", "13.48%", "0%"]
denovo_cols = ["MutationType", "SBS96A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
for ind in range(5, 0, -1):
basis_names = basis_names[:ind]
weights = weights[:ind]
denovo_cols = ["MutationType", "SBS96A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SBS96.pdf"))
return time.time() - s
def gen_SBS1536():
np.random.seed(1234567)
s = time.time()
merger = PdfWriter()
file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS1536.txt"
file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/Decomposed_Solution_Signatures_SBS1536.txt"
denovo_mtx = pd.read_csv(file1, sep="\t")
basis_mtx = pd.read_csv(file2, sep="\t")
output_path = "TestOutput/Results/"
project = "test_run"
mtype = "1536"
denovo_name = "SBS1536A"
basis_names = ["SBS1", "SBS2", "SBS5", "SBS13", "SBS15", "SBS18"]
weights = ["0.94%", "48.72%", "28.44%", "8.42%", "13.48%", "0%"]
denovo_cols = ["MutationType", "SBS1536A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
# sp.run_PlotDecomposition(denovo_mtx, basis_names, weights, output_path, project, mtype, True, statistics, "COSMICv3-GRCh37", "This is where a custom message would go.")
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
for ind in range(5, 0, -1):
basis_names = basis_names[:ind]
weights = weights[:ind]
denovo_cols = ["MutationType", "SBS1536A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SBS1536.pdf"))
return time.time() - s
def gen_SBS288():
np.random.seed(1234567)
s = time.time()
merger = PdfWriter()
file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS288.txt"
file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_SBS288_Signatures.txt"
denovo_mtx = pd.read_csv(file1, sep="\t")
basis_mtx = pd.read_csv(file2, sep="\t")
output_path = "TestOutput/Results/"
project = "test_run"
mtype = "288"
denovo_name = "SBS288A"
basis_names = ["SBS1", "SBS2", "SBS4", "SBS5", "SBS8", "SBS90"]
weights = ["0.94%", "48.72%", "28.44%", "8.42%", "13.48%", "0%"]
denovo_cols = ["MutationType", "SBS288A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
for ind in range(5, 0, -1):
basis_names = basis_names[:ind]
weights = weights[:ind]
denovo_cols = ["MutationType", "SBS288A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SBS288.pdf"))
return time.time() - s
def gen_ID83():
np.random.seed(1234567)
s = time.time()
merger = PdfWriter()
file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_INDEL.txt"
file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_ID83_Signatures.txt"
denovo_mtx = pd.read_csv(file1, sep="\t")
basis_mtx = pd.read_csv(file2, sep="\t")
output_path = "TestOutput/Results/"
project = "test_run"
mtype = "83"
denovo_name = "ID83A"
basis_names = ["ID1", "ID2", "ID4", "ID5", "ID8", "ID9"]
weights = ["0.94%", "48.72%", "28.44%", "8.42%", "13.48%", "0%"]
denovo_cols = ["MutationType", "ID83A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
for ind in range(5, 0, -1):
basis_names = basis_names[:ind]
weights = weights[:ind]
denovo_cols = ["MutationType", "ID83A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
merger.write(os.path.join(output_path, "Result_Decomposition_Plots_ID83.pdf"))
return time.time() - s
def gen_DBS78():
np.random.seed(1234567)
s = time.time()
merger = PdfWriter()
file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_DINUC.txt"
file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_DBS78_Signatures.txt"
denovo_mtx = pd.read_csv(file1, sep="\t")
basis_mtx = pd.read_csv(file2, sep="\t")
output_path = "TestOutput/Results/"
project = "test_run"
mtype = "78"
denovo_name = "DBS78A"
basis_names = ["DBS1", "DBS2", "DBS4", "DBS5", "DBS8", "DBS9"]
weights = ["0.94%", "48.72%", "28.44%", "8.42%", "13.48%", "0%"]
denovo_cols = ["MutationType", "DBS78A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
for ind in range(5, 0, -1):
basis_names = basis_names[:ind]
weights = weights[:ind]
denovo_cols = ["MutationType", "DBS78A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
merger.write(os.path.join(output_path, "Result_Decomposition_Plots_DBS78.pdf"))
return time.time() - s
def gen_CNV48():
np.random.seed(1234567)
s = time.time()
merger = PdfWriter()
file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/CNV48_De-Novo_Signatures.txt"
file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_CNV48_Signatures.txt"
denovo_mtx = pd.read_csv(file1, sep="\t")
basis_mtx = pd.read_csv(file2, sep="\t")
output_path = "TestOutput/Results/"
project = "test_run"
mtype = "48"
denovo_name = "CNV48A"
# basis_names = ["CN1", "CN2", "CN9", "CN20", "CNV48B", "CNV48C"]
basis_names = ["CN1", "CN2", "CN9", "CN20", "CN3", "CN4"]
weights = ["0.94%", "48.72%", "28.44%", "8.42%", "13.48%", "0%"]
denovo_cols = ["MutationType", "CNV48A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
# sp.run_PlotDecomposition(denovo_mtx, basis_names, weights, output_path, project, mtype, True, statistics, "COSMICv3-GRCh37", "This is where a custom message would go.")
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
for ind in range(5, 0, -1):
basis_names = basis_names[:ind]
weights = weights[:ind]
denovo_cols = ["MutationType", "CNV48A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
merger.write(os.path.join(output_path, "Result_Decomposition_Plots_CNV48.pdf"))
return time.time() - s
def gen_SV32():
np.random.seed(1234567)
s = time.time()
merger = PdfWriter()
file1 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/SV32_De-Novo_Signatures.txt"
file2 = "SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_SV32_Signatures.txt"
denovo_mtx = pd.read_csv(file1, sep="\t")
basis_mtx = pd.read_csv(file2, sep="\t")
output_path = "TestOutput/Results/"
project = "test_run"
mtype = "32"
denovo_name = "SV32A"
basis_names = ["SV1", "SV2", "SV3", "SV4", "SV5", "SV6", "SV7", "SV9"]
weights = ["10%", "10%", "10%", "10%", "10%", "10%", "10%", "20%"]
denovo_cols = ["MutationType", "SV32A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
# sp.run_PlotDecomposition(denovo_mtx, basis_names, weights, output_path, project, mtype, True, statistics, "COSMICv3-GRCh37", "This is where a custom message would go.")
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
for ind in range(5, 0, -1):
basis_names = basis_names[:ind]
weights = weights[:ind]
denovo_cols = ["MutationType", "SV32A"]
basis_cols = basis_names.copy()
basis_cols.insert(0, "MutationType")
nonzero_exposures = np.random.uniform(size=len(basis_names))
result = sp.run_PlotDecomposition(
denovo_mtx[denovo_cols],
denovo_name,
basis_mtx[basis_cols],
basis_names,
weights,
nonzero_exposures,
output_path,
project,
mtype,
)
result.seek(0)
reader = PdfReader(result)
for page in reader.pages:
merger.add_page(page)
merger.write(os.path.join(output_path, "Result_Decomposition_Plots_SV32.pdf"))
return time.time() - s
if __name__ == "__main__":
print("Running SBS matrix input tests...")
cosmic_fit_SBS_matrix_test()
decompose_fit_SBS_matrix_test()
denovo_fit_SBS_matrix_test()
print("Running DBS matrix input tests...")
cosmic_fit_DBS_matrix_test()
decompose_fit_DBS_matrix_test()
denovo_fit_DBS_matrix_test()
print("Running ID matrix input tests...")
cosmic_fit_ID_matrix_test()
decompose_fit_ID_matrix_test()
denovo_fit_ID_matrix_test()
print("Running VCF input tests...")
cosmic_fit_vcf_test()
decompose_fit_vcf_test()
denovo_fit_vcf_test()
print("Running SV matrix input tests...")
cosmic_fit_SV_matrix_test()
decompose_fit_SV_matrix_test()
denovo_fit_SV_matrix_test()
print("Running CNV matrix input tests...")
cosmic_fit_CNV_matrix_test()
decompose_fit_CNV_matrix_test()
denovo_fit_CNV_matrix_test()
print("Decomposition Plot tests...")
time_96 = gen_SBS96()
print("Completed SBS96 plots in", time_96, "seconds.")
time_288 = gen_SBS288()
print("Completed SBS288 plots in", time_288, "seconds.")
time_1536 = gen_SBS1536()
print("Completed SBS1536 plots in", time_1536, "seconds.")
time_78 = gen_DBS78()
print("Completed DBS78 plots in", time_78, "seconds.")
time_83 = gen_ID83()
print("Completed ID83 plots in", time_83, "seconds.")
time_48 = gen_CNV48()
print("Completed CNV48 plots in", time_48, "seconds.")
time_32 = gen_SV32()
print("Completed SV32 plots in", time_32, "seconds.")