def test_make_data_directory(self):
new_dir = os.path.join(TestChromosome.TEST_DATA_DIR, "test")
self.assertFalse(os.path.isdir(new_dir))
os.environ['DATA_DIR_VARIABLE'] = new_dir
get_data_directory()
self.assertTrue(os.path.isdir(new_dir))
os.rmdir(new_dir)
def test_make_data_directory(self):
new_dir = os.path.join(TestChromosome.TEST_DATA_DIR, "test")
self.assertFalse(os.path.isdir(new_dir))
os.environ[DATA_DIR_VARIABLE] = new_dir
get_data_directory()
self.assertTrue(os.path.isdir(new_dir))
os.rmdir(new_dir)
def test_get_data_directory(self):
data_dir = get_data_directory()
self.assertEqual(TestChromosome.TEST_DATA_DIR, data_dir)
def test_file_names(self):
for accession in BUILD38_ACCESSIONS.values():
fasta = os.path.join(get_data_directory(), str(accession) + ".fa")
self.assertTrue(os.path.isfile(fasta), fasta)
class TestBuild37(TestCase):
GRCH37_PATH = os.path.join(get_data_directory(), 'homo_sapiens_GRCh37')
def test_file_count(self):
file_count = len(
fnmatch.filter(os.listdir(TestBuild37.GRCH37_PATH), '*.fa'))
self.assertEqual(file_count, 25)
def test_file_names(self):
for name in BUILD37_CHROMOSOMES.keys():
fasta = os.path.join(TestBuild37.GRCH37_PATH,
"chr" + str(name) + ".fa")
self.assertTrue(os.path.isfile(fasta))
# all test sequences were extracted from https://genome.ucsc.edu/ using the
# chromosome browser tool
def test_chr_start_sequences(self):
test_str = "N" * 20
for name in BUILD37_CHROMOSOMES.keys():
# these chromosomes do not have telomeres
if name == 'MT' or name == '17':
continue
seq = Chromosome(name).sequence(0, 20)
self.assertEqual(seq, test_str)
def test_chr1_sequence(self):
expected_seq = "AATCTAAAAAACTGTCAGAT"
seq = Chromosome(1).sequence(243400000, 243400020)
self.assertEqual(expected_seq, seq)
def test_chr2_sequence(self):
expected_seq = "tgtccacgcgcggatgtcgt"
seq = Chromosome(2).sequence(237513040, 237513060)
self.assertEqual(expected_seq, seq)
def test_chr3_sequence(self):
expected_seq = "ctctttcgcccaggctggag"
seq = Chromosome(3).sequence(190352536, 190352556)
self.assertEqual(expected_seq, seq)
def test_chr4_sequence(self):
expected_seq = "ttggagccaaggtctcactc"
seq = Chromosome(4).sequence(184622015, 184622035)
self.assertEqual(expected_seq, seq)
def test_chr5_sequence(self):
expected_seq = "CTTTACTCCACTCATATTCT"
seq = Chromosome(5).sequence(158879589, 158879609)
self.assertEqual(expected_seq, seq)
def test_chr6_sequence(self):
expected_seq = "AGGTGGTAGCCCAGTGGTGC"
seq = Chromosome(6).sequence(158882594, 158882614)
self.assertEqual(expected_seq, seq)
def test_chr7_sequence(self):
expected_seq = "CTTGCTCTCATCCTCCGGGT"
seq = Chromosome(7).sequence(158896447, 158896467)
self.assertEqual(expected_seq, seq)
def test_chr8_sequence(self):
expected_seq = "CTGTCTCCACTGCAGGGCTC"
seq = Chromosome(8).sequence(139508913, 139508933)
self.assertEqual(expected_seq, seq)
def test_chr9_sequence(self):
expected_seq = "GAGGAGAACATTTGCCTGCA"
seq = Chromosome(9).sequence(140705912, 140705932)
self.assertEqual(expected_seq, seq)
def test_chr10_sequence(self):
expected_seq = "TCTGCAGGGGGCGGAGGAAA"
seq = Chromosome(10).sequence(121086020, 121086040)
self.assertEqual(expected_seq, seq)
def test_chr11_sequence(self):
expected_seq = "CTGAGGGTGGCGCTCTCCCC"
seq = Chromosome(11).sequence(132812820, 132812840)
self.assertEqual(expected_seq, seq)
def test_chr12_sequence(self):
expected_seq = "CCTCATGCCCAGTTCTACGT"
seq = Chromosome(12).sequence(132824462, 132824482)
self.assertEqual(expected_seq, seq)
def test_chr13_sequence(self):
expected_seq = "GAAAAGAATTCAAAGAACAC"
seq = Chromosome(13).sequence(113086756, 113086776)
self.assertEqual(expected_seq, seq)
def test_chr14_sequence(self):
expected_seq = "GCAACGGGGTGGTCATCCAC"
seq = Chromosome(14).sequence(105204712, 105204732)
self.assertEqual(expected_seq, seq)
def test_chr15_sequence(self):
expected_seq = "ttcaatcactgatacccttt"
seq = Chromosome(15).sequence(99921491, 99921511)
self.assertEqual(expected_seq, seq)
def test_chr16_sequence(self):
expected_seq = "CTTTCAGCACAGGGCTGTGA"
seq = Chromosome(16).sequence(89862313, 89862333)
self.assertEqual(expected_seq, seq)
def test_chr17_sequence(self):
expected_seq = "TGGAGCTGGAGCCACAGGTC"
seq = Chromosome(17).sequence(80014178, 80014198)
self.assertEqual(expected_seq, seq)
def test_chr18_sequence(self):
expected_seq = "CGAACACTTCGTTGTCCTCT"
seq = Chromosome(18).sequence(74778253, 74778273)
self.assertEqual(expected_seq, seq)
def test_chr19_sequence(self):
expected_seq = "GGCTGGTTAAACTCGGGGTC"
seq = Chromosome(19).sequence(55798374, 55798394)
self.assertEqual(expected_seq, seq)
def test_chr20_sequence(self):
expected_seq = "CTGCCCAAGTGCTCCTGGAG"
seq = Chromosome(20).sequence(55803284, 55803304)
self.assertEqual(expected_seq, seq)
def test_chr21_sequence(self):
expected_seq = "GGCTGGTGTGGCACATGATG"
seq = Chromosome(21).sequence(46074515, 46074535)
self.assertEqual(expected_seq, seq)
def test_chr22_sequence(self):
expected_seq = "AGACGCCGCCCCTGTTCATG"
seq = Chromosome(22).sequence(50552076, 50552096)
self.assertEqual(expected_seq, seq)
def test_chrX_sequence(self):
expected_seq = "GCAAGCAGCAGGATGGGGCC"
seq = Chromosome("X").sequence(152811545, 152811565)
self.assertEqual(expected_seq, seq)
def test_chrY_sequence(self):
expected_seq = "CTGAACGTGCTGAGTTACAG"
seq = Chromosome("Y").sequence(25325643, 25325663)
self.assertEqual(expected_seq, seq)
def test_chrMT_sequence(self):
expected_seq = "TATTGTACGGTACCATAAAT"
seq = Chromosome("MT").sequence(16121, 16141)
self.assertEqual(expected_seq, seq)
def test_get_data_directory(self):
data_dir = get_data_directory()
self.assertEqual(TestChromosome.TEST_DATA_DIR, data_dir)
class TestBuild38(TestCase):
GRCH38_PATH = os.path.join(get_data_directory(), 'homo_sapiens_GRCh38')
def test_file_count(self):
file_count = len(fnmatch.filter(os.listdir(TestBuild38.GRCH38_PATH), '*.fa'))
self.assertEqual(file_count, 25)
def test_file_names(self):
for name in BUILD38_CHROMOSOMES.keys():
fasta = os.path.join(TestBuild38.GRCH38_PATH,
"chr" + str(name) + ".fa")
self.assertTrue(os.path.isfile(fasta))
# all test sequences were extracted from https://genome.ucsc.edu/ using the
# chromosome browser tool
def test_chr_start_sequences(self):
test_str = "N" * 20
for name in BUILD38_CHROMOSOMES.keys():
# these chromosomes do not have telomeres
if name == 'MT'or name == '17':
continue
seq = Chromosome(name, assembly=BUILD38).sequence(0, 20)
self.assertEqual(seq, test_str)
def test_chr1_sequence(self):
expected_seq = "ACAGGAAAAAGATAGCATTC"
seq = Chromosome(1, assembly=BUILD38).sequence(243415701, 243415721)
self.assertEqual(expected_seq, seq)
def test_chr2_sequence(self):
expected_seq = "GCTGGGCCTGAACTGATATC"
seq = Chromosome(2, assembly=BUILD38).sequence(237518537, 237518557)
self.assertEqual(expected_seq, seq)
def test_chr3_sequence(self):
expected_seq = "GCTGAAGTCATCGATGTGAG"
seq = Chromosome(3, assembly=BUILD38).sequence(175256410, 175256430)
self.assertEqual(expected_seq, seq)
def test_chr4_sequence(self):
expected_seq = "CTGtttctgaccacagcctc"
seq = Chromosome(4, assembly=BUILD38).sequence(184624738, 184624758)
self.assertEqual(expected_seq, seq)
def test_chr5_sequence(self):
expected_seq = "CTGTCAATTATCACTGGATC"
seq = Chromosome(5, assembly=BUILD38).sequence(159073395, 159073415)
self.assertEqual(expected_seq, seq)
def test_chr6_sequence(self):
expected_seq = "GATGCACGCTGCTGTTTTAT"
seq = Chromosome(6, assembly=BUILD38).sequence(155144605, 155144625)
self.assertEqual(expected_seq, seq)
def test_chr7_sequence(self):
expected_seq = "GAGCTGGTGGGGAGTAACCC"
seq = Chromosome(7, assembly=BUILD38).sequence(154446213, 154446233)
self.assertEqual(expected_seq, seq)
def test_chr8_sequence(self):
expected_seq = "atcgtggcgtgttctgcagg"
seq = Chromosome(8, assembly=BUILD38).sequence(132447200, 132447220)
self.assertEqual(expected_seq, seq)
def test_chr9_sequence(self):
expected_seq = "GAACCCTCTCATCGTCAAGG"
seq = Chromosome(9, assembly=BUILD38).sequence(132410447, 132410467)
self.assertEqual(expected_seq, seq)
def test_chr10_sequence(self):
expected_seq = "TTCAGGTTCCTTTGCAGCTC"
seq = Chromosome(10, assembly=BUILD38).sequence(122849420, 122849440)
self.assertEqual(expected_seq, seq)
def test_chr11_sequence(self):
expected_seq = "TTTTTAAATGAGTATCCTGG"
seq = Chromosome(11, assembly=BUILD38).sequence(122850195, 122850215)
self.assertEqual(expected_seq, seq)
def test_chr12_sequence(self):
expected_seq = "CATCCCCAGTTTCCCGCGGG"
seq = Chromosome(12, assembly=BUILD38).sequence(122850834, 122850854)
self.assertEqual(expected_seq, seq)
def test_chr13_sequence(self):
expected_seq = "CCCCCCGAAAAGGGCAAAGG"
seq = Chromosome(13, assembly=BUILD38).sequence(113089709, 113089729)
self.assertEqual(expected_seq, seq)
def test_chr14_sequence(self):
expected_seq = "CCCATGTAGTCCAGGTCAGA"
seq = Chromosome(14, assembly=BUILD38).sequence(100353686, 100353706)
self.assertEqual(expected_seq, seq)
def test_chr15_sequence(self):
expected_seq = "attaaaatcatccaatttcc"
seq = Chromosome(15, assembly=BUILD38).sequence(86987986, 86988006)
self.assertEqual(expected_seq, seq)
def test_chr16_sequence(self):
expected_seq = "TTTCAAGCCACAGTCGAGGA"
seq = Chromosome(16, assembly=BUILD38).sequence(83670789, 83670809)
self.assertEqual(expected_seq, seq)
def test_chr17_sequence(self):
expected_seq = "aaacatcatctctaccaaaa"
seq = Chromosome(17, assembly=BUILD38).sequence(80014178, 80014198)
self.assertEqual(expected_seq, seq)
def test_chr18_sequence(self):
expected_seq = "TGCAAAGAGAAATCCTTgga"
seq = Chromosome(18, assembly=BUILD38).sequence(67834418, 67834438)
self.assertEqual(expected_seq, seq)
def test_chr19_sequence(self):
expected_seq = "CTGGGCTGCAGAATCGCTGG"
seq = Chromosome(19, assembly=BUILD38).sequence(45500047, 45500067)
self.assertEqual(expected_seq, seq)
def test_chr20_sequence(self):
expected_seq = "ATGAGATGGACCAAACGCCC"
seq = Chromosome(20, assembly=BUILD38).sequence(59743106, 59743126)
self.assertEqual(expected_seq, seq)
def test_chr21_sequence(self):
expected_seq = "GGCCCCCCCGGACCACCAGG"
seq = Chromosome(21, assembly=BUILD38).sequence(45497642, 45497662)
self.assertEqual(expected_seq, seq)
def test_chr22_sequence(self):
expected_seq = "CTTTTCATTAACTGGATAAA"
seq = Chromosome(22, assembly=BUILD38).sequence(43711474, 43711494)
self.assertEqual(expected_seq, seq)
def test_chrX_sequence(self):
expected_seq = "GGACAACACCtgttaggggc"
seq = Chromosome("X", assembly=BUILD38).sequence(152811545, 152811565)
self.assertEqual(expected_seq, seq)
def test_chrY_sequence(self):
expected_seq = "CAGACCTTCTGCAGTGCACC"
seq = Chromosome("Y", assembly=BUILD38).sequence(25325643, 25325663)
self.assertEqual(expected_seq, seq)
def test_chrMT_sequence(self):
expected_seq = "ATTGTACGGTACCATAAATA"
seq = Chromosome("MT", assembly=BUILD38).sequence(16121, 16141)
self.assertEqual(expected_seq, seq)
def test_file_names(self):
for accession in BUILD37_ACCESSIONS.values():
fasta = os.path.join(get_data_directory(), str(accession) + ".fa")
self.assertTrue(os.path.isfile(fasta), fasta)