def test_fetch():
# mutagene -v fetch cohorts MSKCC --cohort paac_jhu_2014
cli_test_utils.run_with_args('fetch', ['cohorts', 'MSKCC', '--cohort', 'paac_jhu_2014'])
file_name = 'paac_jhu_2014.tar.gz'
os.rename(f'./{file_name}', f'{cli_test_utils.TEST_DIR}/{file_name}')
file_md5sum = cli_test_utils.md5sum(f'{cli_test_utils.TEST_DIR}/{file_name}')
assert file_md5sum == 'b7709f55eaeade1b1c6102d134b16c18'
def test_signature(artifactory_circleci):
infile = f'{cli_test_utils.TEST_DIR}/sample1.maf'
outfile = f'{cli_test_utils.TEST_DIR}/cli-signature-sample1.txt'
genome = f'{cli_test_utils.TEST_DIR}/hg19.2bit'
# mutagene -v signature identify -i sample1.maf -g hg19 -s5 -o test-reports/cli-signature-sample1.txt
cli_test_utils.run_with_args('signature', ['identify', '-i', infile, '-o', outfile, '-g', genome, '-s5'])
out_lines = cli_test_utils.get_file_lines(outfile, 2)
assert out_lines[1].startswith('TCGA-50-6593-01A-11D-1753-08\tMGA-1\t0.532422\t180')
def test_rank(artifactory_circleci):
infile = DEFAULT_INFILE
outfile = f'{cli_test_utils.TEST_DIR}/cli-rank-sample1-pancancer.txt'
genome = DEFAULT_GENOME
cli_test_utils.run_with_args(
'rank', ['-i', infile, '-o', outfile, '-g', genome, '-c', 'pancancer'])
out_lines = cli_test_utils.get_file_lines(outfile, 2)
assert out_lines[1].startswith('CPXM2\tT536M\t')
def test_motif_5_2(artifactory_circleci):
infile = DEFAULT_INFILE
outfile = f'{cli_test_utils.TEST_DIR}/cli-motif-sample1-CA_T.txt'
genome = DEFAULT_GENOME
cli_test_utils.run_with_args(
'motif', ['-i', infile, '-o', outfile, '-g', genome, '-m', '"C[A>T]"'])
statinfo = os.stat(outfile)
assert statinfo.st_size == 0
def test_rank_4_1(artifactory_circleci):
infile = DEFAULT_INFILE
outfile = f'{cli_test_utils.TEST_DIR}/cli-rank-sample1-gcb_lymphomas.txt'
genome = DEFAULT_GENOME
cli_test_utils.run_with_args(
'rank',
['-i', infile, '-o', outfile, '-g', genome, '-c', 'gcb_lymphomas'])
out_lines = cli_test_utils.get_file_lines(outfile, 2)
assert out_lines[1].startswith('BOD1L\tT2810S\t')
def test_motif_5_1(artifactory_circleci):
infile = DEFAULT_INFILE
outfile = f'{cli_test_utils.TEST_DIR}/cli-motif-sample1.txt'
genome = DEFAULT_GENOME
cli_test_utils.run_with_args(
'motif', ['-i', infile, '-o', outfile, '-g', genome, '--strand', 'A'])
out_lines = cli_test_utils.get_file_lines(outfile, 2)
assert out_lines[1].startswith(
'TCGA-50-6593-01A-11D-1753-08\tC>T in CpG\t[C>T]G\tany strand\t')
def test_fetch():
# mutagene -v fetch cohorts MSKCC --cohort paac_jhu_2014
cli_test_utils.run_with_args('fetch', ['cohorts', 'MSKCC', '--cohort', 'paac_jhu_2014'])
file_name = 'paac_jhu_2014.tar.gz'
os.rename(f'./{file_name}', f'{cli_test_utils.TEST_DIR}/{file_name}')
# Removed due to inconsistent md5 sums across repeated downloads, affecting both this test and CircleCI
#file_md5sum = cli_test_utils.md5sum(f'{cli_test_utils.TEST_DIR}/{file_name}')
#assert file_md5sum == 'acbf8c569c2b8f5684ccfb1e036743f0'
file_size = os.path.getsize(f'{cli_test_utils.TEST_DIR}/{file_name}')
assert file_size == 271932
def test_profile(artifactory_circleci):
infile = 'tests/motifs/data/vcf/data.vcf'
outfile = f'{cli_test_utils.TEST_DIR}/cli-profile-test.txt'
genome = f'{cli_test_utils.TEST_DIR}/hg19.2bit' # 'tests/motifs/data/test_genome.2bit'
# mutagene -v profile -i sample1.maf -g hg19 -o test-reports/cli-profile-sample1.txt
cli_test_utils.run_with_args('profile', ['-i', infile, '-o', outfile, '-g', genome])
out_lines = cli_test_utils.get_file_lines(outfile, 3)
assert out_lines[0] == 'A[C>A]A\t0\n'
assert out_lines[1] == 'A[C>G]A\t2\n'
assert out_lines[2] == 'A[C>T]A\t4\n'