def test_compute_cn(output_folder):
if solver_available():
main(args=[
'-x',
f'{output_folder}/results',
'-i',
f'{this_dir}/data/bbc/bulk',
'-n2',
'-p',
'100',
'-v',
'3',
'-u',
'0.03',
'-r',
'6700', # random seed
'-j',
'8',
'-eD',
'6',
'-eT',
'12',
'-g',
'0.35',
'-l',
'0.6'
])
df1 = pd.read_csv(f'{output_folder}/results/best.bbc.ucn', sep='\t')
df2 = pd.read_csv(f'{this_dir}/data/results/best.bbc.ucn', sep='\t')
assert_frame_equal(df1, df2)
def test_solve_command_gurobi(output_folder):
old_value = config.compute_cn.solver
config.compute_cn.solver = 'gurobi'
main(args=[
'-x',
os.path.join(output_folder), '-i',
os.path.join(this_dir, 'data/bulk'), '-n2', '-p', '400', '-v', '3',
'-u', '0.03', '--mode', '1', '-r', '6700', '-j', '8', '-eD', '6',
'-eT', '12', '-g', '0.35', '-l', '0.6'
])
df1 = pd.read_csv(os.path.join(output_folder, 'best.bbc.ucn'), sep='\t')
df2 = pd.read_csv(os.path.join(this_dir, 'data', 'best.bbc.ucn'), sep='\t')
assert_frame_equal(df1, df2)
config.compute_cn.solver = old_value
def test_script(_, bams, output_folder):
normal_bam, tumor_bams = bams
binBAM(
args=[
'-N', normal_bam,
'-T'
] + tumor_bams + [
'-b', '50kb',
'-st', config.paths.samtools,
'-S', 'Normal', 'Tumor1', 'Tumor2', 'Tumor3',
'-g', config.paths.reference,
'-j', '12',
'-q', '11',
'-O', os.path.join(output_folder, 'bin/normal.1bed'),
'-o', os.path.join(output_folder, 'bin/bulk.1bed'),
'-v'
]
)
SNPCaller(
args=[
'-N', normal_bam,
'-r', config.paths.reference,
'-c', '290', # min reads
'-C', '300', # max reads
'-R', '',
'-o', os.path.join(output_folder, 'snps'),
'-st', config.paths.samtools,
'-bt', config.paths.bcftools,
'-j', '1'
]
)
deBAF(
args=[
'-bt', config.paths.bcftools,
'-st', config.paths.samtools,
'-N', normal_bam,
'-T'
] + tumor_bams + [
'-S', 'Normal', 'Tumor1', 'Tumor2', 'Tumor3',
'-r', config.paths.reference,
'-j', '12',
'-q', '11',
'-Q', '11',
'-U', '11',
'-c', '8',
'-C', '300',
'-O', os.path.join(output_folder, 'baf/normal.1bed'),
'-o', os.path.join(output_folder, 'baf/bulk.1bed'),
'-L', os.path.join(output_folder, 'snps', 'chr22.vcf.gz'),
'-v'
]
)
_stdout = sys.stdout
sys.stdout = StringIO()
comBBo(args=[
'-c', os.path.join(output_folder, 'bin/normal.1bed'),
'-C', os.path.join(output_folder, 'bin/bulk.1bed'),
'-B', os.path.join(output_folder, 'baf/bulk.1bed'),
'-e', '12'
])
out = sys.stdout.getvalue()
sys.stdout.close()
sys.stdout = _stdout
with open(os.path.join(output_folder, 'bb/bulk.bb'), 'w') as f:
f.write(out)
cluBB(args=[
os.path.join(output_folder, 'bb/bulk.bb'),
'-o', os.path.join(output_folder, 'bbc/bulk.seg'),
'-O', os.path.join(output_folder, 'bbc/bulk.bbc'),
'-e', '22171', # random seed
'-tB', '0.04',
'-tR', '0.15',
'-d', '0.4'
])
df1 = pd.read_csv(os.path.join(output_folder, 'bbc/bulk.seg'), sep='\t')
df2 = pd.read_csv(os.path.join(this_dir, 'data', 'bulk.seg'), sep='\t')
assert_frame_equal(df1, df2)
BBot(args=[
os.path.join(output_folder, 'bbc/bulk.bbc'),
'--rundir', os.path.join(output_folder, 'plots')
])
if os.getenv('GRB_LICENSE_FILE') is not None:
main(args=[
SOLVE,
'-x', os.path.join(output_folder, 'results'),
'-i', os.path.join(output_folder, 'bbc/bulk'),
'-n2',
'-p', '400',
'-v', '3',
'-u', '0.03',
'-r', '6700', # random seed
'-j', '8',
'-eD', '6',
'-eT', '12',
'-g', '0.35',
'-l', '0.6'
])
df1 = pd.read_csv(os.path.join(output_folder, 'results/best.bbc.ucn'), sep='\t')
df2 = pd.read_csv(os.path.join(this_dir, 'data', 'best.bbc.ucn'), sep='\t')
assert_frame_equal(df1, df2)
BBeval(args=[
os.path.join(output_folder, 'results/best.bbc.ucn'),
'--rundir', os.path.join(output_folder, 'evaluation')
])