def test_file5():
popset = load_csv(TESTFILE5,
header = 1, # number of rows to skip for header info
hvr1 = 1, # column number if present
hvr1_covers = [16090,16365],
add16k = True, # add 16000 to every hvr1 site?
haplogroup = 0, # column number if present
n = 2, # column number(s) if present
population = "Yemenite Jews", # column number or name or if pop_with_n is True,
# names to go with N columns
)
for line, error in popset.errors:
print "%d: %s: %s" % (line, error.message, error.expression)
assert not popset.errors
def test_file2():
popset = load_csv(TESTFILE2,
header = 1, # number of rows to skip for header info
hvr1 = 1, # column number if present
hvr1_covers = [16000,16400],
add16k = True, # add 16000 to every hvr1 site?
rflps = 2, # column number if present
rflp_format = 1, # 1. +/- POSITION ENZYME (i.e. "+16389 HinfI")
haplogroup = 3, # column number if present
sample_id = 0, # column number if present
haplotype_id = False, # column number if present
n = 4, # column number if present
population = 5, # column number(s) if present
)
for line, error in popset.errors:
print "%d: %s: %s" % (line, error.message, error.expression)
assert not popset.errors
def test_file3():
popset = load_csv(TESTFILE3,
header = 1, # number of rows to skip for header info
hvr1 = 1, # column number if present
hvr1_covers = [16030,16370],
add16k = True, # add 16000 to every hvr1 site?
rflps = [2,3,4,5,6,7,8], # column number(s) if present
rflp_format = 2, # 2. '+' present; '-' absent; '#' or '' not tested
sites = False, # column number(s) if present
sites_on_rCRS = False, # matched entry or list for sites columns
haplogroup = 14, # column number if present
sample_id = False, # column number if present
haplotype_id = 0, # column number if present
pop_with_n = True, # are N's arranged by population?
n = [9,10,11,12], # column number(s) if present
population = ["YTA","YTI","YHG","YHA"], # column number or name or if pop_with_n is True,
# names to go with N columns
)
for line, error in popset.errors:
print "%d: %s: %s" % (line, error.message, error.expression)
assert not popset.errors
def test_file4():
popset = load_csv(TESTFILE4,
header = 1, # number of rows to skip for header info
hvr1 = 1, # column number if present
hvr1_covers = [16024,16383],
add16k = True, # add 16000 to every hvr1 site?
rflps = range(5,13), # column number if present
rflp_format = 2, # 2. '+' present; '-' absent; '#' or '' not tested
sites = [13,14], # column number(s) if present
sites_on_rCRS = [769,1018], # matched entry or list for sites columns
haplogroup = 4, # column number if present
sample_id = 0, # column number if present
sample_id_sep = ',', # what separates multiple ids?
haplotype_id = False, # column number if present
pop_with_n = False, # are N's arranged by population?
n = 2, # column number(s) if present
population = 15, # column number or name or if pop_with_n is True,
# names to go with N columns
)
for line, error in popset.errors:
print "%d: %s: %s" % (line, error.message, error.expression)
assert not popset.errors
def test_file1():
popset = load_csv(TESTFILE1,
header = 2, # number of rows to skip for header info
hvr1 = 3, # column number if present
hvr1_covers = [16000,16569],
add16k = True, # add 16000 to every hvr1 site?
hvr2 = 4, # column number if present
hvr2_covers = [1,400],
sites = range(5,32), # column number(s) if present
sites_on_rCRS = [3834,6386,6962,7028,8618,8860,8701,10398,10400,10873,11914,11929,12308,12372,12705,14766,15849,15850,15884,15896,15907,15924,15928,15940,15954,15968,15992], # matched entry or list for sites columns
haplogroup = 0, # column number if present
sample_id = 1, # column number if present
n = 32, # column number if present
population = 'Saudi Arabia',
)
for line, error in popset.errors:
print "%d: %s: %s" % (line, error.message, error.expression)
assert not popset.errors
# the coverage for the population is the intersection of all the coverages of all the
# samples in that population. In this case, none of the additional sites were typed
# in ALL of the samples
should_cover=Coverage((16000,16569),(1,400))
print "should cover: '%s' - does cover: '%s'" % (should_cover, popset.coverage)
assert popset.coverage == should_cover
assert popset.populations[0].coverage == should_cover
# make sure that a selection of the samples have their appropriate coverage
# sample '27' was typed for 7028, 12308, 12372 as well
should_cover=Coverage((16000,16569),(1,400),7028,12308,12372)
sample_coverage = popset.populations[0].sample_by_id('27').coverage
print "should cover: '%s' - does cover: '%s'" % (should_cover, sample_coverage)
assert sample_coverage == should_cover
# sample '223' was typed for only 7028 as well
should_cover=Coverage((16000,16569),(1,400),7028)
sample_coverage = popset.populations[0].sample_by_id('223').coverage
print "should cover: '%s' - does cover: '%s'" % (should_cover, sample_coverage)
assert sample_coverage == should_cover
# sample '50' was typed for 11929, 12308, 12372 as well
should_cover=Coverage((16000,16569),(1,400),11929,12308,12372)
sample_coverage = popset.populations[0].sample_by_id('50').coverage
print "should cover: '%s' - does cover: '%s'" % (should_cover, sample_coverage)
assert sample_coverage == should_cover
# sample '201' was typed for 6962, 7028, 10398, 10400, 10873, 12705, 15884, 15896 as well
should_cover=Coverage((16000,16569),(1,400),6962,7028,10398,10400,10873,12705,15884,15896)
sample_coverage = popset.populations[0].sample_by_id('201').coverage
print "should cover: '%s' - does cover: '%s'" % (should_cover, sample_coverage)
assert sample_coverage == should_cover
assert popset.num_populations == 1
assert popset.num_samples == 120
pop = popset.populations[0]
haps = ['H'] * 15 + ['I'] + ['J'] * 7 + ['J1'] * 4 + ['J1b'] * 14 + ['J1d'] * 2 + \
['K'] * 7 + ['L2a1a','L2a2','L2c2','L3d1','L3f','L3h1','L3h1','L3i','M'] + \
['M1a'] * 4 + ['M1b1','M25','M3'] + ['N1a'] * 5 + ['N1b'] * 3 + ['N1c'] * 2 + \
['preHV'] * 21 + ['T','T1'] + ['T3'] * 4 + \
['T5'] * 2 + ['U1a'] * 2 + ['U1b','U2e'] + ['U3'] * 2 + \
['U5a1a','U6a','U8b','U9','U9','U9','W','X','X']
for i in range(popset.num_samples):
print pop.samples[i].haplogroup, haps[i]
assert pop.samples[i].haplogroup == haps[i]
# check that the population name is correctly assigned while we're looping
# through the samples anyways
assert pop.samples[i].population == 'Saudi Arabia'
