def test_merge_two_files(self):
result = merge_files(tu.abs_path('misc/geneset1.txt'), tu.abs_path('misc/geneset2.txt'))
assert_equal(list(result),
['1 2 x2 y2 z3 x2 y2 z8',
'2 3 x1 y1 z4 x1 y1 z10',
'1 1 x1 y1 z6 x4 y5 z9',
'2 4 x2 y2 z5 x2 y2 z12'], 'wrong merge result')
def test_neighbors(self):
'''Test retrieving node's pedigree neighbors.'''
p = itu.Templates.problem_hut()
node = 1298
expected = np.genfromtxt(tu.abs_path('ibd_distant/nbhrs_' + repr(node) + '.txt'), dtype=int).tolist()
tu.assert_equal_as_sets(p.pedigree.neighbors(node, 4, False), expected, 'Incorrect genotyped neighbor list')
expected = np.genfromtxt(tu.abs_path('ibd_distant/nbhrs_' + repr(node) + '_genotyped.txt'), dtype=int).tolist()
tu.assert_equal_as_sets(p.pedigree.neighbors(node, 4, True), expected, 'Incorrect genotyped neighbor list')
def test_neighbors(self):
'''Test retrieving node's pedigree neighbors.'''
p = itu.Templates.problem_hut()
node = 1298
expected = np.genfromtxt(tu.abs_path('ibd_distant/nbhrs_' +
repr(node) + '.txt'),
dtype=int).tolist()
tu.assert_equal_as_sets(p.pedigree.neighbors(node, 4, False), expected,
'Incorrect genotyped neighbor list')
expected = np.genfromtxt(tu.abs_path('ibd_distant/nbhrs_' +
repr(node) + '_genotyped.txt'),
dtype=int).tolist()
tu.assert_equal_as_sets(p.pedigree.neighbors(node, 4, True), expected,
'Incorrect genotyped neighbor list')
def setUp(self):
'''Load segments from a test file.'''
self.segments = map(lambda line: map(int, line),
csv.reader(open(tu.abs_path('segment/segments-0-100.out'), 'rb'),
delimiter=' ', skipinitialspace=True))
self.num_samples = 1415
start, stop, min_len = 0, 99, 0.4 * MEGA_BASE_PAIR
self.selected_segments = it.ifilter(lambda line: max(start, line[0]) < min(stop, line[1])
and line[3] - line[2] >= min_len,
self.segments)
class TestItemUtil(unittest.TestCase):
#---------------------------------------------
# Constants
#---------------------------------------------
__FILE = tu.abs_path('misc/hutt.chr22.snplist')
#---------------------------------------------
# Test Methods
#---------------------------------------------
def test_file_line_selection(self):
'''Test selecting lines from a file.'''
f = open(TestItemUtil.__FILE, 'rb')
num_lines = iu.ilen(f)
assert_equal(num_lines, 3218, 'Wrong item count')
f = open(TestItemUtil.__FILE, 'rb')
a = list(iu.linerange(f, 0, num_lines, 100))
assert_equal(len(a), 33, 'Wrong item range')
assert_equal(a[0], 'SNP_A-2141031', 'Wrong item')
assert_equal(a[-1], 'rs2015453', 'Wrong item')
def test_segment_range(self):
'''Test getting the start and end of equidistant intervals in an item collection.'''
# Non-divisible case
self.__test_segment_range(100, 7, 1)
# Divisible case
self.__test_segment_range(100, 10, 1)
# Less trivial item list
self.__test_segment_range(100, 7, 2)
self.__test_segment_range(100, 10, 2)
def test_groupby_with_range(self):
'''Test the groupby_with_range() function.'''
assert_equal(iu.groupby_with_range(''), [])
assert_equal(iu.groupby_with_range('AAAABBBCCDAABBB'),
[('A', (0, 3)),
('B', (4, 6)),
('C', (7, 8)),
('D', (9, 9)),
('A', (10, 11)),
('B', (12, 14))])
#---------------------------------------------
# Private Methods
#---------------------------------------------
def __test_segment_range(self, n, step, c):
'''Test getting the start and end of equidistant intervals in an item collection.'''
items = np.arange(0, n, c)
segments = iu.segmentrange(items, step)
assert_equal(segments[:, 0], range(0, n, c * step), 'Wrong start array')
assert_equal(segments[:, 1],
range(c * (step - 1), n, c * step) + ([n - c] if np.mod(n, step) else []),
'Wrong end array')
def setUp(self):
'''Load segments from a test file.'''
self.segments = map(
lambda line: map(int, line),
csv.reader(open(tu.abs_path('segment/segments-0-100.out'), 'rb'),
delimiter=' ',
skipinitialspace=True))
self.num_samples = 1415
start, stop, min_len = 0, 99, 0.4 * MEGA_BASE_PAIR
self.selected_segments = it.ifilter(
lambda line: max(start, line[0]) < min(stop, line[1]) and line[3] -
line[2] >= min_len, self.segments)
def setUp(self):
'''Use a localhost UCSC copy.'''
self.idcoef_dao = IdCoefDao(tu.abs_path('pedigree/example.id'))
self.kinship_dao = KinshipDao(tu.abs_path('pedigree/example.kinship'))
Created on May 31, 2012
@author: Oren Livne <*****@*****.**>
============================================================
'''
import networkx as nx, numpy as np, test_util as tu
from numpy.testing.utils import assert_equal
from impute.data.problem import Problem
from impute.data import io, io_pedigree, io_genotype
from impute.phasing.examples import OUT_PHASING
#---------------------------------------------
# Constants
#---------------------------------------------
'''Hutterites pedigree - test file name. This file was obtained from Jessica and Gaixin
(minped.3671).'''
HUTT_PED = tu.abs_path('pedigree/hutterites.tfam')
HUTT_GENOTYPED_PED = tu.abs_path('pedigree/hutterites.genotyped.tfam')
'''Small test pedigree'''
SMALL_FILE = tu.abs_path('network/small.tfam')
'''Genotype hutt data with 1 SNP'''
GENOTYPE_SAMPLE = tu.abs_path('sample/sample')
'''Synthetic data on a duo (proband + single parent) with several SNPs'''
GENOTYPE_DUO = tu.abs_path('duo/duo')
# Contains solution to the trio phasing problem: parent genotypes and child haplotypes
GENOTYPE_DUO_SOLUTION = tu.abs_path('duo/duo_solution')
'''Synthetic data on a trio (proband + parents) with several SNPs'''
GENOTYPE_TRIO = tu.abs_path('trio/trio')
# Contains solution to the trio phasing problem: parent genotypes and child haplotypes
def setUp(self):
'''Use a localhost UCSC copy.'''
self.idcoef_dao = IdCoefDao(tu.abs_path('pedigree/example.id'))
self.kinship_dao = KinshipDao(tu.abs_path('pedigree/example.kinship'))
Created on May 31, 2012
@author: Oren Livne <*****@*****.**>
============================================================
'''
import networkx as nx, numpy as np, test_util as tu
from numpy.testing.utils import assert_equal
from impute.data.problem import Problem
from impute.data import io, io_pedigree, io_genotype
from impute.phasing.examples import OUT_PHASING
#---------------------------------------------
# Constants
#---------------------------------------------
'''Hutterites pedigree - test file name. This file was obtained from Jessica and Gaixin
(minped.3671).'''
HUTT_PED = tu.abs_path('pedigree/hutterites.tfam')
HUTT_GENOTYPED_PED = tu.abs_path('pedigree/hutterites.genotyped.tfam')
'''Small test pedigree'''
SMALL_FILE = tu.abs_path('network/small.tfam')
'''Genotype hutt data with 1 SNP'''
GENOTYPE_SAMPLE = tu.abs_path('sample/sample')
'''Synthetic data on a duo (proband + single parent) with several SNPs'''
GENOTYPE_DUO = tu.abs_path('duo/duo')
# Contains solution to the trio phasing problem: parent genotypes and child haplotypes
GENOTYPE_DUO_SOLUTION = tu.abs_path('duo/duo_solution')
'''Synthetic data on a trio (proband + parents) with several SNPs'''
GENOTYPE_TRIO = tu.abs_path('trio/trio')
# Contains solution to the trio phasing problem: parent genotypes and child haplotypes
GENOTYPE_TRIO_SOLUTION = tu.abs_path('trio/trio_solution')
'''Data on all SNPs and a single nuclear family. If not otherwise specified, data is from chr22.'''
FAMILY7 = tu.abs_path('family7/family7')
def test_hash_file(self):
result = hash_file(tu.abs_path('misc/geneset1.txt'), ' ', [0, 1])
assert_equal(result, [(3, 4), (1, 1), (1, 2), (2, 3), (2, 4)], 'file hash is wrong')
