def testPedCompleteAlternateIteration(self):
"""Useful if you need to iterate over these in a more controlled manner"""
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
index = 0
snp = next(ped_parser.__iter__())
try:
while True:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertEqual(self.genotypes[index],
list(snp.genotype_data))
index += 1
next(snp)
except StopIteration:
pass
self.assertEqual(7, index)
def testPedCompleteAlternateIteration(self):
"""Useful if you need to iterate over these in a more controlled manner"""
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 0
snp = ped_parser.__iter__().next()
try:
while True:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertEqual(self.genotypes[index], list(snp.genotype_data))
index += 1
snp.next()
except StopIteration:
pass
self.assertEqual(7, index)
