def test_access(self):
fasta = "formats/chrM-Y-trunc.hg19.fa"
for min_gap_size, expect_nrows in ((None, 3), (500, 3), (1000, 2)):
acc = commands.do_access(fasta, [], min_gap_size)
self.assertEqual(len(acc), expect_nrows)
excludes = ["formats/dac-my.bed", "formats/duke-my.bed"]
for min_gap_size, expect_nrows in ((None, 5), (2, 5), (20, 4),
(200, 3), (2000, 2)):
commands.do_access(fasta, excludes, min_gap_size)
def test_access(self):
fasta = "formats/chrM-Y-trunc.hg19.fa"
for min_gap_size, expect_nrows in ((None, 7), (500, 3), (1000, 2)):
acc = commands.do_access(fasta, [],
min_gap_size,
skip_noncanonical=False)
self.assertEqual(len(acc), expect_nrows)
excludes = ["formats/dac-my.bed", "formats/my-targets.bed"]
for min_gap_size, expect_nrows in ((None, 12), (2, 10), (20, 5),
(200, 3), (2000, 2)):
acc = commands.do_access(fasta,
excludes,
min_gap_size,
skip_noncanonical=False)
self.assertEqual(len(acc), expect_nrows)
# Dropping chrM, keeping only chrY
acc = commands.do_access(fasta, excludes, 10, skip_noncanonical=True)
self.assertEqual(len(acc), 5)
def test_access(self):
fasta = "formats/chrM-Y-trunc.hg19.fa"
for min_gap_size, expect_nrows in ((None, 7),
(500, 3),
(1000, 2)):
acc = commands.do_access(fasta, [], min_gap_size,
skip_noncanonical=False)
self.assertEqual(len(acc), expect_nrows)
excludes = ["formats/dac-my.bed", "formats/my-targets.bed"]
for min_gap_size, expect_nrows in ((None, 12),
(2, 10),
(20, 5),
(200, 3),
(2000, 2)):
acc = commands.do_access(fasta, excludes, min_gap_size,
skip_noncanonical=False)
self.assertEqual(len(acc), expect_nrows)
# Dropping chrM, keeping only chrY
acc = commands.do_access(fasta, excludes, 10,
skip_noncanonical=True)
self.assertEqual(len(acc), 5)