def create_test_array():
d = {'9':'5', '10':'288', '11':'002556688', '12':'00012355555',
'13':'0000013555688', '14':'00002555558',
'15':'0000000000355555555557', '16':'000045', '17':'000055',
'18':'0005', '19':'00005', '21':'5'}
ext_array = IntsStats()
for key, values in d.items():
for num in values:
ext_array.append(int(key+num))
return ext_array
def test_distribution(self):
'It tests the histogram function'
# ints_array = IntsStats(1)
# num_integers = 1000000
# max_value = 100000
# for i in xrange(num_integers):
# ints_array.append(random.randint(0, max_value))
# (distrib, bin_edges) = ints_array.histogram(25)
#
# (distrib, bin_edges) = ints_array.histogram(25, range_=None)
#
# (distrib, bin_edges) = ints_array.histogram(25, range_=(None, 1000))
#
# (distrib, bin_edges) = ints_array.histogram(25, range_=(1000, None))
#
# (distrib, bin_edges) = ints_array.histogram(25, range_=(1000, 2000))
ints_array = self.create_test_array()
distrib = ints_array.calculate_distribution(bins=10,
remove_outliers=5)
assert distrib['distrib'] == [7L, 13L, 7L, 10L, 7L, 22L, 6L, 4L, 5L, 5L]
assert distrib['bin_edges'] == [110, 118, 126, 134, 142, 150, 158, 166,
174, 182, 190]
general_stats = '''Statistics for histogram
-------------------------
minimum: 95
maximum: 215
average: 145.1522
variance: 557.4334
sum: 13354
items: 92'''
result_fhand = tempfile.NamedTemporaryFile()
ints_array.write_general_stats(result_fhand)
assert general_stats in open(result_fhand.name).read()
ints_array = IntsStats([0, 0, 1, 3])
assert [2, 1, 1] == ints_array.calculate_distribution(bins=3)['distrib']
def _get_lengths_quals_from_file(seq_fpath):
'Given a sequence file it returns the lengths and quals'
lengths = IntsStats(init_len=1000)
quals = IntsStats(init_len=100)
for seq in seqs_in_file(open(seq_fpath)):
lengths.append(len(seq))
qual = seq.qual
if qual:
quals.extend(qual)
return lengths, quals
def test_array():
'Create an extensible array'
ext_array = IntsStats(init_len=5)
ext_array.append(6)
ext_array.append(2)
assert ext_array.min == 2
assert ext_array.max == 6
ext_array.append(200)
assert ext_array.max == 200
input_ = (3, 5, 7, 7, 38)
ext_array = IntsStats(input_)
assert ext_array.median == 7
def test_stats_functs(self):
'It test the statistical functions of the class'
ext_array = IntsStats()
ext_array.append(3)
ext_array.append(5)
ext_array.append(7)
ext_array.append(7)
ext_array.append(38)
assert ext_array.median == 7
ext_array = IntsStats()
ext_array.append(3)
ext_array.append(5)
ext_array.append(7)
ext_array.append(7)
assert ext_array.median == 6
ext_array = self.create_test_array()
assert ext_array.median == 145
assert round(ext_array.average, 2) == 145.15
assert ext_array.sum == 13354
assert ext_array.count == 92
assert round(ext_array.variance, 2) == 557.43
