def test_two_insertions_in_one_position():
assert len(str2sites('16129.1A 16129.2A')) == 2
assert 16129 == str2sites('16129.1A 16129.2A')[0].position
assert str2sites('16129.1A 16129.2A')[0].insert in [1,2]
def test_two_insertions_in_plus_format():
assert len(str2sites('16129+AA')) == 2
def test_two_insertions_in_plus_format_add16k():
assert len(str2sites('129+AA',True)) == 2
if hvr2:
try:
polys = str2sites(l[hvr2])
polymorphisms += polys
except MtconvertError, e:
errors.append( (line_number, e) )
if sites:
for i in range(0,len(sites)):
site_index = sites[i]
position = sites_on_rCRS[i]
value = l[site_index].strip().upper()
if value in ('A','G','C','T'):
try:
poly = str2sites('%d%s' % (position,value))
polymorphisms.append(poly)
this_sample_segments.append(position)
except MtconvertError, e:
errors.append( (line_number, e) )
coverage = Coverage(*this_sample_segments)
###################################################
# Extract haplogroup
###################################################
hap = None
if haplogroup is not False:
hap = l[haplogroup].strip()
def test_transition_without_value_add16k():
assert 16129 == str2sites('129',True)[0].position
assert 'C' == str2sites('129',True)[0].value
def test_commas_spaces_and_semicolons():
assert 'G' == str2sites('16293G, 16311C; 16129')[0].value
assert 'C' == str2sites('16293G, 16311C; 16129')[1].value
def test_single_substitution_add16k():
assert 16129 == str2sites('129A',add16k=True)[0].position
assert 'A' == str2sites('129A',add16k=True)[0].value
def test_deletion_in_del_and_value_format():
assert '-' == str2sites('16129delA')[0].value
def test_insertion_in_standard_format():
assert 1 == str2sites('16129.1A')[0].insert
def test_deletion_in_standard_format():
assert '-' == str2sites('16129d')[0].value
def test_deletion_in_standard_format_add16k():
assert '-' == str2sites('129d',True)[0].value
def test_deletion_in_minus_format_add16k():
assert '-' == str2sites('129-',True)[0].value
def test_deletion_in_minus_format():
assert '-' == str2sites('16129-')[0].value
def test_empty_string():
assert [] == str2sites('')
def test_two_insertions_in_one_position_add16k():
assert len(str2sites('129.1A 129.2A', True)) == 2
assert 16129 == str2sites('129.1A 129.2A', True)[0].position
assert str2sites('129.1A 129.2A', True)[0].insert in [1,2]
def test_insertion_in_standard_format_add16k():
assert 1 == str2sites('129.1A',True)[0].insert
def test_spaces():
assert len(str2sites('16293G 16311C')) == 2
assert 'G' == str2sites('16293G 16311C')[0].value
assert 'C' == str2sites('16293G 16311C')[1].value
def test_single_substitution():
assert 16129 == str2sites('16129A')[0].position
assert 'A' == str2sites('16129A')[0].value
def test_out_of_order_insertions():
assert len(str2sites('1.2A 1.1A')) == 2
def test_insertion_in_plus_format():
assert 1 == str2sites('16129+A')[0].insert
def test_10_insertions():
s = '1.1A 1.2A 1.3A 1.4A 1.5A 1.6A 1.7A 1.8A 1.9A 1.10A'
assert len(str2sites(s)) == 10
def test_insertion_in_plus_format_add16k():
assert 1 == str2sites('129+A',True)[0].insert
def load_csv(file,
header = 1, # number of rows to skip for header info
hvr1 = False, # column number if present
hvr1_covers = [16024,16365],
add16k = True, # add 16000 to every hvr1 site?
hvr2 = False, # column number if present
hvr2_covers = [73,340],
rflps = False, # column number if present
rflp_format = False, # ? how to implement this ?
sites = False, # column number(s) if present
sites_on_rCRS = [], # matched entry or list for sites columns
haplogroup = False, # column number if present
sample_id = False, # 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 = False, # column number(s) if present
population = False, # column number or name or if pop_with_n is True,
# names to go with N columns
doi = False,
pmid = False,
):
"""Load mitochondrial haplotype definitions from csv file.
Column numbers are to be provided in python-standard 0-based counting.
"""
if population is False:
population = "Unknown"
errors = []
line_number = header
if sites:
if len(sites) != len(sites_on_rCRS):
errors.append((0, MtconvertError("When sites are included, sites_on_rCRS must match")))
# base coverage is given by hvr1 and hvr2 covers
segments = list(x for x in [hvr1_covers, hvr2_covers] if x)
# every sample needs an id,
# if it is given in the file, we use that
# otherwise create one in the format 's#'
if sample_id is not False:
def sample_generator(line):
sids = line[sample_id].split(sample_id_sep)
for sid in sids:
yield (sid, population)
else:
def sample_generator(line):
global s
count = 0
pop_names = []
if pop_with_n:
max = sum(num(line[x]) for x in n)
for i in range(len(n)):
pop_names = pop_names + [population[i]] * num(line[n[i]])
elif n:
max = num(line[n])
pop_names = [population] * max
else:
max = 1
pop_names = [population]
while count < max:
pop = pop_names[count]
count += 1
s += 1
yield ("s%d" % s, pop)
# start the reader
reader = csv.reader(open(file, 'rU'))
samples = []
for l in list(x for x in reader)[header:]:
line_number += 1
###################################################
# Read in polymorphism data
###################################################
polymorphisms = []
this_sample_segments = list(x for x in segments)
if hvr1:
try:
polys = str2sites(l[hvr1], add16k=add16k)
polymorphisms += polys
except MtconvertError, e:
errors.append( (line_number, e) )
if hvr2:
try:
polys = str2sites(l[hvr2])
polymorphisms += polys
except MtconvertError, e:
errors.append( (line_number, e) )
def test_transition_without_value():
assert 16129 == str2sites('16129')[0].position
assert 'C' == str2sites('16129')[0].value