def test_uas_all(tmp_path):
inputdb = data_file('snps')
exp_out = data_file('snps_uas_all.txt')
obs_out = str(tmp_path / 'uas.txt')
arglist = ['snps', inputdb, '-o', obs_out, '--type', 'all', '--uas']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.snps.main(args)
assert filecmp.cmp(exp_out, obs_out) is True
def test_format_straitrazor(input, testoutput):
with NamedTemporaryFile() as outfile:
inputdb = data_file(input)
testformat = data_file(testoutput)
arglist = ['format', inputdb, '-o', outfile.name]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.format.main(args)
assert filecmp.cmp(testformat, outfile.name) is True
def test_format_sex_loci_straitrazor(tmp_path):
inputdb = data_file('STRait_Razor_test_output')
exp_out = data_file('testformat_sr_sexloci.csv')
obs_out = str(tmp_path / 'sr.csv')
obs_out_sex = str(tmp_path / 'sr_sexloci.csv')
arglist = ['format', inputdb, '-o', obs_out, '--include-sex']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.format.main(args)
assert filecmp.cmp(exp_out, obs_out_sex) is True
def test_format():
UAStestfile = data_file(
'snps/Positive Control Sample Details Report 2315.xlsx')
formatoutput = data_file('testformat.csv')
with NamedTemporaryFile(suffix='.csv') as outfile:
arglist = ['format', UAStestfile, '-o', outfile.name, '--uas']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.format.main(args)
assert filecmp.cmp(formatoutput, outfile.name) is True
def test_powerseq_flanking_anno():
with NamedTemporaryFile(suffix='.txt') as outfile:
input = data_file('powerseq_flanking_anno_test.csv')
test_powerseq = data_file(
'powerseq_flanking_anno_test_flanks_anno.txt')
arglist = ['annotate', input, '-o', outfile.name, '--kit', 'powerseq']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.annot.main(args)
outfile_name = os.path.splitext(outfile.name)[0]
outfile_name_output = f'{outfile_name}_flanks_anno.txt'
assert filecmp.cmp(test_powerseq, outfile_name_output) is True
def test_sr_all(tmp_path):
inputdb = data_file('snps')
exp_out = data_file('snps_sr_all.txt')
exp_out_full = data_file('snps_sr_all_full_output.txt')
obs_out = str(tmp_path / 'sr.txt')
obs_out_full = str(tmp_path / 'sr_full_output.txt')
arglist = ['snps', inputdb, '-o', obs_out, '--type', 'all']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.snps.main(args)
assert filecmp.cmp(exp_out, obs_out) is True
assert filecmp.cmp(exp_out_full, obs_out_full) is True
def test_uas_directory_with_xy(tmp_path):
inputdb = data_file('UAS_bulk_input')
exp_out_auto = data_file('UAS_bulk_test.csv')
exp_out_sex = data_file('UAS_bulk_test_sexloci.csv')
obs_out_auto = str(tmp_path / 'format_output.csv')
obs_out_sex = str(tmp_path / 'format_output_sexloci.csv')
arglist = ['format', '-o', obs_out_auto, '--uas', '--include-sex', inputdb]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.format.main(args)
assert filecmp.cmp(exp_out_auto, obs_out_auto) is True
assert filecmp.cmp(exp_out_sex, obs_out_sex) is True
def test_format_stdout(capsys):
UAStestfile = data_file(
'snps/Positive Control Sample Details Report 2315.xlsx')
formatoutput = data_file('testformat.csv')
arglist = ['format', UAStestfile, '--uas']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.format.main(args)
with open(formatoutput, 'r') as fh:
exp_out = fh.read().strip()
terminal = capsys.readouterr()
obs_out = terminal.out.strip()
assert obs_out == exp_out
def test_annotate_uas():
with NamedTemporaryFile() as outfile:
os.unlink(outfile.name)
inputfile = data_file('2800M_formatted_uas.csv')
testanno = data_file('2800M_uas_anno.txt')
arglist = [
'annotate', inputfile, '-o', outfile.name, '--kit', 'forenseq',
'--uas'
]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.annot.main(args)
assert filecmp.cmp(testanno, outfile.name) is True
def test_format_sexloci_uas():
UAStestfile = data_file(
'snps/Positive Control Sample Details Report 2315.xlsx')
formatoutput = data_file('testformat_uas_sexloci.csv')
with NamedTemporaryFile(suffix='.csv') as outfile:
arglist = [
'format', UAStestfile, '-o', outfile.name, '--uas', '--include-sex'
]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.format.main(args)
outfile_name = os.path.splitext(outfile.name)[0]
outfile_name_output = f'{outfile_name}_sexloci.csv'
assert filecmp.cmp(formatoutput, outfile_name_output) is True
def test_uas_directory_autosomal_only(tmp_path):
inputdb = data_file('UAS_bulk_input')
copydb = str(tmp_path / 'UAS_bulk_input')
copytree(inputdb, copydb)
bogusfile = os.path.join(copydb, 'bogusfile.txt')
with open(bogusfile, 'w') as fh:
pass
exp_out_auto = data_file('UAS_bulk_test.csv')
obs_out_auto = str(tmp_path / 'format_output.csv')
arglist = ['format', '-o', obs_out_auto, '--uas', copydb]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.format.main(args)
assert filecmp.cmp(exp_out_auto, obs_out_auto) is True
def test_annotate_uas_sexloci():
with NamedTemporaryFile() as outfile:
os.unlink(outfile.name)
inputfile = data_file('testformat_uas.csv')
testanno = data_file('testformat_uas_sexloci.txt')
arglist = [
'annotate', inputfile, '-o', outfile.name, '--kit', 'forenseq',
'--uas', '--include-sex'
]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.annot.main(args)
outfile_name = os.path.splitext(outfile.name)[0]
outfile_name_output = f'{outfile_name}_sexloci.txt'
assert filecmp.cmp(testanno, outfile_name_output) is True
def test_annotate_full_nocombine(infile, len_sum, len_uncom, xy_len_sum,
xy_len_uncom, kit):
inputfile = data_file(infile)
with NamedTemporaryFile() as outfile:
arglist_nocomb = [
'annotate', inputfile, '-o', outfile.name, '--kit', kit,
'--nocombine', '--include-sex'
]
args_nocomb = lusSTR.cli.get_parser().parse_args(arglist_nocomb)
lusSTR.annot.main(args_nocomb)
outfile_name = os.path.splitext(outfile.name)[0]
with open(f'{outfile_name}_no_combined_reads.txt', 'r') as fh:
assert len(fh.readlines()) == len_uncom
with open(f'{outfile_name}_sexloci_no_combined_reads.txt', 'r') as fh:
assert len(fh.readlines()) == xy_len_uncom
arglist_comb = [
'annotate', inputfile, '-o', outfile.name, '--kit', kit,
'--include-sex'
]
args_comb = lusSTR.cli.get_parser().parse_args(arglist_comb)
lusSTR.annot.main(args_comb)
with open(outfile.name, 'r') as fh:
assert len(fh.readlines()) == len_sum
with open(f'{outfile_name}_sexloci.txt', 'r') as fh:
assert len(fh.readlines()) == xy_len_sum
def test_annotate_sr_sexloci(inputfile, testoutput, flank_output, kit):
with NamedTemporaryFile() as outfile:
os.unlink(outfile.name)
inputfile = data_file(inputfile)
testanno = data_file(testoutput)
flankanno = data_file(flank_output)
arglist = [
'annotate', inputfile, '-o', outfile.name, '--kit', kit,
'--include-sex'
]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.annot.main(args)
outfile_name = os.path.splitext(outfile.name)[0]
outfile_name_output = f'{outfile_name}_sexloci.txt'
assert filecmp.cmp(testanno, outfile_name_output) is True
flank_outfile = f'{outfile_name}_sexloci_flanks_anno.txt'
assert filecmp.cmp(flankanno, flank_outfile) is True
def test_uas_type(type, lines, tmp_path):
inputdb = data_file('snps')
obs_out = str(tmp_path / 'uas.txt')
arglist = ['snps', inputdb, '-o', obs_out, '--type', type, '--uas']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.snps.main(args)
with open(obs_out, 'r') as fh:
assert len(fh.readlines()) == lines
def test_FGA_short_seq():
with NamedTemporaryFile(suffix='.txt') as outfile:
input = data_file('test_FGA_short_seq.csv')
arglist = ['annotate', input, '-o', outfile.name, '--kit', 'forenseq']
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.annot.main(args)
with open(outfile.name, 'r') as fh:
assert len(fh.readlines()) == 1
def test_annotate_combine():
with NamedTemporaryFile() as outfile:
inputfile = data_file('Flanks_testing_file.csv')
arglist = [
'annotate', inputfile, '-o', outfile.name, '--kit', 'forenseq'
]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.annot.main(args)
with open(outfile.name, 'r') as fh:
assert len(fh.readlines()) == 952
def test_sr_type(type, lines, full_lines, tmp_path):
inputdb = data_file('snps')
obs_out = str(tmp_path / 'sr.txt')
obs_out_full = str(tmp_path / 'sr_full_output.txt')
arglist = ['snps', inputdb, '-o', obs_out, '--type', type]
args = lusSTR.cli.get_parser().parse_args(arglist)
lusSTR.snps.main(args)
with open(obs_out, 'r') as fh:
assert len(fh.readlines()) == lines
with open(obs_out_full, 'r') as fh:
assert len(fh.readlines()) == full_lines