def test_lookup(capsys):
arglist = ['lookup', 'rs10815466']
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
out, err = capsys.readouterr()
assert 'mh09KK-033 MHDBM-8458b727 GRCh38 chr9 680713,680762,680790 2.9343 0.1008 0.0504 ALFRED' in out
assert ' mh09AT-15 MHDBM-b46abf2e GRCh38 chr9 680713,680762,680767,680790 2.9471 0.1160 0.0602 ISFG2019:P597' in out
def test_main_no_args(capsys):
with pytest.raises(SystemExit):
args = get_parser().parse_args([])
microhapdb.cli.main(args)
terminal = capsys.readouterr()
message = 'show this help message and exit'
assert message in terminal.out or message in terminal.err
def test_main_marker_query(capsys):
args = get_parser().parse_args(['marker', '--query', 'Chrom == "chr19"'])
microhapdb.cli.main(args)
terminal = capsys.readouterr()
exp_out = '''
Name PermID Reference Chrom Offsets Ae In Fst Source
mh19USC-19pA MHDBM-2d713eab GRCh38 chr19 561778,561795,561815 2.7453 0.0870 0.0733 10.1016/j.fsigen.2019.102213
mh19KK-056 MHDBM-d6ff8635 GRCh38 chr19 4852124,4852324 2.4391 0.0773 0.1760 ALFRED
mh19CP-007 MHDBM-49dbcc57 GRCh38 chr19 14310739,14310772,14310780 3.0813 0.0466 0.0776 ALFRED
mh19USC-19pB MHDBM-76427274 GRCh38 chr19 16040864,16040894,16040899,16040921,16040929 3.5107 0.1647 0.0731 10.1016/j.fsigen.2019.102213
mh19ZHA-006 MHDBM-5f597339 GRCh38 chr19 20579862,20579863,20579879,20579892,20579916,20579924 3.8739 0.1681 -0.0032 10.1016/j.fsigen.2020.102255
mh19NH-23 MHDBM-dd72537b GRCh38 chr19 22052723,22052774,22052817 1.9380 0.0414 -0.0124 10.1016/j.legalmed.2015.06.003
mh19KKCS-299 MHDBM-a70896aa GRCh38 chr19 22546697,22546702,22546748,22546779,22546810,22546829,22546850 NaN NaN NaN 10.1016/j.fsigen.2020.102275
mh19KK-299 MHDBM-8cbeb11c GRCh38 chr19 22546697,22546748,22546779,22546810,22546850 4.1592 0.2335 0.1102 ALFRED
mh19AT-47 MHDBM-8f439540 GRCh38 chr19 22546697,22546748,22546779 2.4025 0.1298 0.1170 ISFG2019:P597
mh19ZHA-007 MHDBM-afb5b4d1 GRCh38 chr19 28397315,28397408,28397447,28397455 3.7262 0.1551 -0.0007 10.1098/rsos.191937
mh19USC-19qA MHDBM-f757e745 GRCh38 chr19 33273771,33273785,33273811,33273816 3.3219 0.1127 0.0880 10.1016/j.fsigen.2019.102213
mh19KK-301 MHDBM-2069446a GRCh38 chr19 50938487,50938502,50938526,50938550 1.9707 0.2673 0.1698 ALFRED
mh19KKCS-300 MHDBM-bc8b7213 GRCh38 chr19 50947786,50947789,50947790,50947830,50947876,50947877,50947967 NaN NaN NaN 10.1016/j.fsigen.2020.102275
mh19KK-057 MHDBM-eb558c37 GRCh38 chr19 51654948,51655025,51655062 2.3266 0.0667 0.0428 ALFRED
mh19ZHA-009 MHDBM-346aa500 GRCh38 chr19 53129072,53129075,53129133,53129203,53129249 3.8739 0.1405 -0.0241 10.1098/rsos.191937
mh19USC-19qB MHDBM-7b40359b GRCh38 chr19 53714387,53714389,53714413 4.0756 0.1368 0.0163 10.1016/j.fsigen.2019.102213
'''
obs_out = terminal.out
print(obs_out)
assert exp_out.strip() == obs_out.strip()
def test_main_marker_noargs(capsys):
args = get_parser().parse_args(['marker'])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
outlines = out.strip().split('\n')
assert len(outlines) == 1 + 198 + 15 + 40 + 26 + (
11 - 1) + 10 + 118 + 90 + 25 + 20 + 23
def test_main_frequency_by_pop(pop, marker, allele, numrows, capsys):
testargs = (pop, marker, allele)
arglist = ['frequency'] + [arg for arg in testargs if arg is not None]
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
outlines = terminal.out.strip().split('\n')
assert len(outlines) == numrows
def test_files(capsys):
with pytest.raises(SystemExit):
args = get_parser().parse_args(['--files'])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
print(err)
outlines = out.strip().split('\n')
assert len(outlines) == 7
def test_main_pop_noargs(capsys):
args = get_parser().parse_args(['population'])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
outlines = out.strip().split('\n')
assert len(
outlines
) == 1 + 96 + 3 + 1 + 1 + 1 + 7 # 1 header line + 96 ALFRED + 3 LOVD + 1 Linköping + 1 NRIPS + 1 Chen2019 + 7 mMHseq
def test_main_marker_region_mode(capsys):
arglist = ['marker', '--region', 'chr15']
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
out, err = capsys.readouterr()
outlines = out.strip().split('\n')
print(out)
assert len(outlines) == 20 + 1 # 17 markers + 1 header line
def test_main_marker_view_bad():
arglist = [
'marker', '--format', 'fasta', '--extend-mode', '5', '--delta', '20',
'--min-length', '175', 'mh01USC-1pD', 'mh22NH-27'
]
args = get_parser().parse_args(arglist)
args.format = 'html'
with pytest.raises(ValueError, match=r'unsupported view format "html"'):
microhapdb.cli.main(args)
def test_main_marker_extendmode_bad(mode, capsys):
arglist = [
'marker', '--format', 'fasta', '--extend-mode', mode, '--delta', '20',
'--min-length', '175', 'mh01USC-1pD', 'mh22NH-27'
]
with pytest.raises(SystemExit):
args = get_parser().parse_args(arglist)
terminal = capsys.readouterr()
assert 'invalid str_to_extend_mode value' in terminal.err
def test_main_marker_extendmode(mode, offsets1, offsets2, capsys):
arglist = [
'marker', '--format', 'fasta', '--extend-mode', mode, '--delta', '20',
'--min-length', '175', 'mh01USC-1pD', 'mh22NH-27'
]
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
assert offsets1 in terminal.out
assert offsets2 in terminal.out
def test_main_marker_panel_region_conflict(capsys):
with NamedTemporaryFile() as panelfile:
with open(panelfile.name, 'w') as fh:
for marker in ['mh05KK-058', 'mh06KK-101', 'mh20KK-035']:
print(marker, file=fh)
arglist = ['marker', '--panel', panelfile.name, '--region=chr12']
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
assert 'ignoring user-supplied marker IDs in --region mode' in terminal.err
def test_main_panel(panel, capsys):
arglist = [
'marker', '--panel', panel + '_legacy', '--format=fasta', '--delta=25',
'--min-length=250'
]
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
testout = data_file('tests/panel-' + panel + '.fasta')
print(terminal.out)
with open(testout, 'r') as fh:
assert fh.read().strip() == terminal.out.strip()
def test_main_pop_query(capsys):
args = get_parser().parse_args(
['population', '--query', 'Source == "10.1016/j.fsigen.2018.05.008"'])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
testout = '''
ID Name Source
MHDBP-3dab7bdd14 Africa 10.1016/j.fsigen.2018.05.008
MHDBP-936bc36f79 Asia 10.1016/j.fsigen.2018.05.008
MHDBP-383d86606a NL 10.1016/j.fsigen.2018.05.008
'''
print(out)
assert testout.strip() == out.strip()
def test_hg37_detail(capsys):
arglist = ['marker', '--format=detail', '--GRCh37', 'mh17USC-17pA']
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
exp_out = '''
--------------------------------------------------------------[ MicroHapDB ]----
mh17USC-17pA a.k.a MHDBM-d5646523
Marker Definition (GRCh37)
Marker extent
- chr17:3821918-3821988 (70 bp)
Target amplicon
- chr17:3918614-3918704 (90 bp)
Constituent variants
- chromosome offsets: 3821918,3821952,3821987
- marker offsets: 0,34,69
- amplicon offsets: 10,44,79
- cross-references: rs4995288, rs4995289, rs9904113
Observed haplotypes
- C,C,A
- C,C,C
- C,T,A
- C,T,C
- T,C,A
- T,C,C
- T,T,A
- T,T,C
--[ Core Marker Sequence ]--
>mh17USC-17pA
CGTCTCATTTGGGGATCTTATCATATCCACAGTGTACCCCAGGGACCTACATTTATTTTCCTGCTGCTGA
--[ Target Amplicon Sequence with Haplotypes ]--
* * *
CCTGGAGCACCGTCTCATTTGGGGATCTTATCATATCCACAGTGTACCCCAGGGACCTACATTTATTTTCCTGCTGCTGATAACTCCACA
..........C.................................C..................................A..........
..........C.................................C..................................C..........
..........C.................................T..................................A..........
..........C.................................T..................................C..........
..........T.................................C..................................A..........
..........T.................................C..................................C..........
..........T.................................T..................................A..........
..........T.................................T..................................C..........
--------------------------------------------------------------------------------
'''
obs_out = terminal.out
assert exp_out.strip() == obs_out.strip()
def test_main_marker_fasta_default_delta(capsys):
args = get_parser().parse_args(
['marker', '--format=fasta', 'mh01CP-016', 'mh06PK-24844'])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
testout = '''
>mh01CP-016 PermID=MHDBM-021e569a GRCh38:chr1:55559012-55559056 variants=18,56,62 Xref=SI664876L
TGGCACACAACAAGTGCTTATAATGAAAGCATTAGTGAGTAAAAGAGTGATCCCTGGCTTTGAACTCCCTCTAAGTGTAC
C
>mh06PK-24844 PermID=MHDBM-aa39cbba GRCh38:chr6:13861392-13861446 variants=13,20,35,42,51,55,59,60,61,67
AGGAAGAAAGTGATTACATCCAAACGTGAGCAGGAGGAAACTCGGAACATACTGTTTTTAAGAACTAGTATCACTAGAGT
T
'''
print(out)
assert testout.strip() == out.strip()
def test_marker_offsets_cli(capsys):
arglist = [
'marker', '--format=offsets', '--delta=25', '--min-length=200',
'mh03AT-09', 'mh11KK-180', 'mh13KK-217', 'mh07USC-7qC'
]
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
result = pandas.read_csv(StringIO(terminal.out), sep='\t')
assert result.shape == (15, 2)
observed = list(result.Offset)
expected = [
85, 114, 66, 95, 122, 123, 134, 25, 145, 203, 218, 25, 65, 179, 217
]
assert observed == expected
def test_parser():
cli = get_parser().parse_args(['marker'])
assert cli.cmd == 'marker'
assert cli.query is None
assert cli.region is None
assert cli.id == []
cli = get_parser().parse_args(['marker', '--region', 'chr5'])
assert cli.cmd == 'marker'
assert cli.query is None
assert cli.region == 'chr5'
assert cli.id == []
cli = get_parser().parse_args(['marker', 'mh04CP-003', 'mh17KK-014'])
assert cli.cmd == 'marker'
assert cli.query is None
assert cli.region is None
assert cli.id == ['mh04CP-003', 'mh17KK-014']
cli = get_parser().parse_args(
['population', '--query', 'Name.str.contains("Amer")'])
assert cli.cmd == 'population'
assert cli.query == 'Name.str.contains("Amer")'
assert cli.id == []
def test_main_marker_panel(capsys):
with NamedTemporaryFile() as panelfile:
with open(panelfile.name, 'w') as fh:
for marker in ['mh15KK-058', 'mh06KK-101', 'mh20KK-035']:
print(marker, file=fh)
arglist = ['marker', '--panel', panelfile.name]
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
testout = '''
Name PermID Reference Chrom Offsets Ae In Fst Source
mh06KK-101 MHDBM-8a2c760e GRCh38 chr6 170280714,170280900 1.6705 0.2296 0.2590 ALFRED
mh15KK-058 MHDBM-d6c594d2 GRCh38 chr15 28120284,28120471,28120586 2.2110 0.3799 0.0862 ALFRED
mh20KK-035 MHDBM-92f3685a GRCh38 chr20 2088698,2088728 2.1328 0.2104 0.2180 ALFRED
'''
print(terminal.out)
assert testout.strip() == terminal.out.strip()
def test_ae_pop(capsys):
arglist = ['marker', '--region=chr18:1-25000000', '--ae-pop=CDX']
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
exp_out = '''
Name PermID Reference Chrom Offsets Ae In Fst Source
mh18PK-87558 MHDBM-1e5374f1 GRCh38 chr18 1960542,1960557,1960561,1960566,1960582,1960588 1.9767 0.1325 0.0494 10.1016/j.fsigen.2018.05.008
mh18USC-18pA MHDBM-56dfa93b GRCh38 chr18 5280017,5280020,5280070,5280071,5280093 1.8402 0.2130 0.1818 10.1016/j.fsigen.2019.102213
mh18CP-005 MHDBM-a85754d3 GRCh38 chr18 8892864,8892893,8892896,8892907 3.3873 0.0904 0.0059 ALFRED
mh18ZBF-002 MHDBM-3702ab96 GRCh38 chr18 11900702,11900723,11900734,11900778 3.2413 0.2019 0.0864 10.1002/elps.201900451
mh18ZHA-004 MHDBM-db649dba GRCh38 chr18 14315931,14315952,14315958,14316046 3.1131 0.1949 0.0118 10.1016/j.fsigen.2020.102255
mh18KK-285 MHDBM-ea520d26 GRCh38 chr18 24557354,24557431,24557447,24557489 2.6188 0.1721 0.0836 ALFRED
mh18AT-38 MHDBM-db09ec41 GRCh38 chr18 24557431,24557447,24557489 2.6144 0.1419 0.0837 ISFG2019:P597
'''
obs_out = terminal.out
print(obs_out)
assert exp_out.strip() == obs_out.strip()
def test_hg37_ae_pop(capsys):
arglist = [
'marker', '--region=chr18:50000000-80000000', '--GRCh37',
'--ae-pop=PJL'
]
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
exp_out = '''
Name PermID Reference Chrom Offsets Ae In Fst Source
mh18USC-18qB MHDBM-14fcada5 GRCh37 chr18 50547498,50547528,50547540 3.8565 0.1449 0.0500 10.1016/j.fsigen.2019.102213
mh18USC-18qC MHDBM-6bf74efc GRCh37 chr18 63842523,63842541,63842557,63842562 3.5570 0.1436 -0.0049 10.1016/j.fsigen.2019.102213
mh18KKCS-293 MHDBM-350bd971 GRCh37 chr18 76089731,76089843,76089884,76089885,76089906,76089944,76089967 NaN NaN NaN 10.1016/j.fsigen.2020.102275
mh18KK-293 MHDBM-13ed6da8 GRCh37 chr18 76089885,76089906,76089944,76089967 2.6445 0.2495 0.0837 ALFRED
mh18AT-39 MHDBM-13ed6da8 GRCh37 chr18 76089885,76089906,76089944,76089967 2.6445 0.2495 0.0837 ISFG2019:P597
'''
obs_out = terminal.out
print(obs_out)
assert exp_out.strip() == obs_out.strip()
def test_hg37(capsys):
arglist = ['marker', '--region=chr18:1-25000000', '--GRCh37']
args = get_parser().parse_args(arglist)
microhapdb.cli.main(args)
terminal = capsys.readouterr()
exp_out = '''
Name PermID Reference Chrom Offsets Ae In Fst Source
mh18PK-87558 MHDBM-1e5374f1 GRCh37 chr18 1960543,1960558,1960562,1960567,1960583,1960589 2.3659 0.1325 0.0494 10.1016/j.fsigen.2018.05.008
mh18USC-18pA MHDBM-56dfa93b GRCh37 chr18 5280016,5280019,5280069,5280070,5280092 3.4330 0.2130 0.1818 10.1016/j.fsigen.2019.102213
mh18CP-005 MHDBM-a85754d3 GRCh37 chr18 8892862,8892891,8892894,8892905 3.6722 0.0904 0.0059 ALFRED
mh18ZBF-002 MHDBM-3702ab96 GRCh37 chr18 11900701,11900722,11900733,11900777 3.2962 0.2019 0.0864 10.1002/elps.201900451
mh18ZHA-004 MHDBM-db649dba GRCh37 chr18 14315930,14315951,14315957,14316045 2.9579 0.1949 0.0118 10.1016/j.fsigen.2020.102255
mh18KK-285 MHDBM-ea520d26 GRCh37 chr18 22137318,22137395,22137411,22137453 2.7524 0.1721 0.0836 ALFRED
mh18AT-38 MHDBM-db09ec41 GRCh37 chr18 22137395,22137411,22137453 2.7093 0.1419 0.0837 ISFG2019:P597
mh18CP-003 MHDBM-6fdf83f9 GRCh37 chr18 23068395,23068425,23068433 3.1124 0.1061 0.0183 ALFRED
mh18ZBF-001 MHDBM-742f43e2 GRCh37 chr18 24223721,24223752 2.9546 0.1796 0.0047 10.1002/elps.201900451
'''
obs_out = terminal.out
print(obs_out)
assert exp_out.strip() == obs_out.strip()
def test_main_marker_fasta_long_delta(capsys):
args = get_parser().parse_args([
'marker', '--format=fasta', '--delta=25', '--min-length=250',
'mh13CP-010', 'mh08PK-46625'
])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
testout = '''
>mh08PK-46625 PermID=MHDBM-840756f3 GRCh38:chr8:1194352-1194371 variants=115,119,127,134
TGCTGGCAAGTTGGAAACACAGGCTCTGCGATTTTGAGAGTGAACCTGCAAGAGACAAGCAGACGTTGGCAGTGCCGCGT
CCCGGCTGGTGGAGGGAGCCCGGATGCCTGGCAGACAGTCAGTGGTCGGTTGGCGGCCGGCCCACATAAGGGCACCATGC
TCACCGTGTCTAGGCAGAGCTGGAGGCTCCTCCTGCCCAGGGCGGCCTCCAGGTGGGGAGGACGGCAGAGCTTCCCTCAG
TCCCACTTTC
>mh13CP-010 PermID=MHDBM-13233c9a GRCh38:chr13:29218044-29218076 variants=109,120,141
AATAAGACCTGGTCTCCACAAAGAAATTTTAAAAATTAGCTGGGCTTGGTGATGCATGCCTGTAGTCCCAGCTACTGAGG
CTGAGGCAGGAGTATTCCTTGAGTCCAGGAGGTCATGGCTGCAGTGAGTTATGATTGTGCCGTCATACTCCAGCCTGAAC
AAAAGAGTGAGACCTTGTCCCTCCCCGCCAAAACCAAACCAAAACAAAACAAAACAAAAAAAAAACACCTAAAAACCCCA
GTGTTTACAGT
'''
print(out)
assert testout.strip() == out.strip()
def test_main_pop_detail(capsys):
args = get_parser().parse_args(
['population', '--format=detail', 'Koreans'])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
assert '876 total allele frequencies available' in out
def test_main_marker_region_mode_failure(capsys):
arglist = ['marker', '--region', 'chr15:']
args = get_parser().parse_args(arglist)
with pytest.raises(ValueError, match=r'cannot parse region "chr15:"'):
microhapdb.cli.main(args)
def test_help(capsys):
with pytest.raises(SystemExit):
get_parser().parse_args(['-h'])
terminal = capsys.readouterr()
message = 'show this help message and exit'
assert message in terminal.out or message in terminal.err
def test_main_marker_detail(capsys):
args = get_parser().parse_args(['marker', '--format=detail', 'mh01CP-008'])
microhapdb.cli.main(args)
out, err = capsys.readouterr()
assert '>mh01CP-008\nGACATCACGCCACTGCT\n' in out
def test_version(capsys):
with pytest.raises(SystemExit):
get_parser().parse_args(['-v'])
terminal = capsys.readouterr()
assert microhapdb.__version__ in terminal.out or microhapdb.__version__ in terminal.err
def test_ae_pop_bad_pop():
arglist = ['marker', '--ae-pop=ABC', 'mh18USC-18pA']
args = get_parser().parse_args(arglist)
with pytest.raises(ValueError, match=r'no Ae data for population "ABC"'):
microhapdb.cli.main(args)
