def test_some_examples():
"""MotifQueryMaker query from pre-aligned sequence"""
qm = MotifQueryMaker()
indian = "TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCCTCA"
ethiopian = "TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCACCTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCCTCA"
indian_query = qm.new_query(indian)
ethiopian_query = qm.new_query(ethiopian)
assert_instance_of(MotifQuery, indian_query)
assert_instance_of(MotifQuery, ethiopian_query)
#assert_equal(360, len(indian_query.all_polymorphisms))
#assert_equal(360, len(ethiopian_query.all_polymorphisms))
assert_equal(2, len(indian_query.defining_polymorphisms))
assert_equal(4, len(ethiopian_query.defining_polymorphisms))
assert Polymorphism(16129,0,'A') in indian_query.defining_polymorphisms
assert Polymorphism(16362,0,'C') in indian_query.defining_polymorphisms
assert Polymorphism(16362,0,'C') in ethiopian_query.defining_polymorphisms
assert Polymorphism(16241,0,'C') in ethiopian_query.defining_polymorphisms
assert Polymorphism(16311,0,'C') in ethiopian_query.defining_polymorphisms
assert Polymorphism(16223,0,'T') in ethiopian_query.defining_polymorphisms
def test_new_query_from_site_str():
"""MotifQueryMaker query from sites string"""
qm = MotifQueryMaker()
sites = '16129A 16362C'
query = qm.new_query_from_sites(sites)
assert_equal(2, len(query.defining_polymorphisms))
print query.defining_polymorphisms
assert Polymorphism(16129,0,'A') in query.defining_polymorphisms
assert Polymorphism(16362,0,'C') in query.defining_polymorphisms
def test_new_queries_from_unaligned_LONG():
"""MotifQueryMaker query from unaligned sequence"""
qm = MotifQueryMaker()
indian = "TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCCTCA"
a_indian = indian[3:-3]
query = qm.new_query(a_indian)
#assert_equal(360, len(query.all_polymorphisms))
assert_equal(2, len(query.defining_polymorphisms))
assert Polymorphism(16129,0,'A') in query.defining_polymorphisms
assert Polymorphism(16362,0,'C') in query.defining_polymorphisms
b_indian = indian[:100] + indian[101:]
query = qm.new_query(b_indian)
assert_equal(3, len(query.defining_polymorphisms))
assert Polymorphism(16129,0,'A') in query.defining_polymorphisms
assert Polymorphism(16362,0,'C') in query.defining_polymorphisms