def test1_encrypt(self):
cmn.sam2bam(self.RESOURCE_PATH + 'encrypt/input.sam',
self.RESOURCE_PATH + 'encrypt/input.bam')
pysam.index(self.RESOURCE_PATH + 'encrypt/input.bam')
Vac.text2vac(self.RESOURCE_PATH + 'encrypt/input.vac.txt',
self.RESOURCE_PATH + 'encrypt/input.vac')
with open(self.RESOURCE_PATH + 'admin', 'r') as key_file, \
open(self.RESOURCE_PATH + 'admin.pub', 'r') as pub_key_file:
rsa_key = RSA.importKey(key_file.read(), passphrase=self.KEY_PASS)
rsa_pub_key = RSA.importKey(pub_key_file.read())
# creates DIFF with secret
self.locker.encrypt(
rsa_sign_key=rsa_key,
rsa_enc_key=rsa_pub_key,
bam_filename=self.RESOURCE_PATH + 'encrypt/input.bam',
vac_filename=self.RESOURCE_PATH + 'encrypt/input.vac',
out_bam_filename=self.RESOURCE_PATH + 'encrypt/output.mut.bam',
out_enc_diff_filename=self.RESOURCE_PATH +
'encrypt/output.diff.enc',
mut_p=0)
pysam.index(self.RESOURCE_PATH + 'encrypt/output.mut.bam')
cmn.bam2sam(self.RESOURCE_PATH + 'encrypt/output.mut.bam',
self.RESOURCE_PATH + 'encrypt/output.mut.sam')
def test_mutate_02(self):
# EOF VAC case
Vac.text2vac(self.RESOURCE_PATH + 'input_02.vac.txt', self.RESOURCE_PATH + 'input_02.vac')
bdiff_file = self._mut.mutate(
vac_filename=self.RESOURCE_PATH + 'input_02.vac',
mut_bam_filename=self.RESOURCE_PATH + 'output_02.bam',
secret=self.SECRET,
mut_p=0,
rng=self._rnd
)
self.assertEqual(21, self._mut.stat(BamMutator.STAT_ALIGNMENT_COUNT))
self.assertEqual(13, self._mut.stat(BamMutator.STAT_COVERING_COUNT))
self.assertEqual(7, self._mut.stat(BamMutator.STAT_VAC_COUNT))
self.assertEqual(6, self._mut.stat(BamMutator.STAT_MUT_COUNT))
self.assertEqual(4, self._mut.stat(BamMutator.STAT_DIFF_COUNT))
self.assertEqual(6, self._mut.stat(BamMutator.STAT_ALIGNMENT_MUT_COUNT))
cmn.bam2sam(self.RESOURCE_PATH + 'output_02.bam', self.RESOURCE_PATH + 'output_02.sam')
self.assertTrue(filecmp.cmp(
self.RESOURCE_PATH + 'desired_02.sam',
self.RESOURCE_PATH + 'output_02.sam'
))
BdiffIO.to_text_file(bdiff_file, self.RESOURCE_PATH + 'output_02.diff.txt')
is_equal = filecmp.cmp(self.RESOURCE_PATH + 'desired_02.diff.txt', self.RESOURCE_PATH + 'output_02.diff.txt')
self.assertTrue(is_equal)
def test_unmutate_01(self):
# all mapped
with BdiffIO.from_text_file(self.RESOURCE_PATH +
'input.diff.txt') as bdiff_file:
self.mut.unmutate(bdiff_file=bdiff_file,
out_bam_filename=self.RESOURCE_PATH +
'output_01.bam')
self.assertEqual(17, self.mut.stat(BamMutator.STAT_ALIGNMENT_COUNT))
self.assertEqual(11, self.mut.stat(BamMutator.STAT_COVERING_COUNT))
self.assertEqual(8, self.mut.stat(BamMutator.STAT_MUT_COUNT))
self.assertEqual(5, self.mut.stat(BamMutator.STAT_DIFF_COUNT))
self.assertEqual(8, self.mut.stat(BamMutator.STAT_ALIGNMENT_MUT_COUNT))
bam2sam(self.RESOURCE_PATH + 'output_01.bam',
self.RESOURCE_PATH + 'output_01.sam')
is_equal = filecmp.cmp(self.RESOURCE_PATH + 'desired_01.sam',
self.RESOURCE_PATH + 'output_01.sam')
self.assertEqual(True, is_equal)
def test_unmutate_05(self):
# include unmapped
with BdiffIO.from_text_file(self.RESOURCE_PATH +
'input.diff.txt') as bdiff_file:
self.mut.unmutate(bdiff_file=bdiff_file,
out_bam_filename=self.RESOURCE_PATH +
'output_05.bam',
include_unmapped=True)
self.assertEqual(21, self.mut.stat(BamMutator.STAT_ALIGNMENT_COUNT))
# one synonymous mutation is present
self.assertEqual(11, self.mut.stat(BamMutator.STAT_COVERING_COUNT))
self.assertEqual(8, self.mut.stat(BamMutator.STAT_MUT_COUNT))
self.assertEqual(5, self.mut.stat(BamMutator.STAT_DIFF_COUNT))
self.assertEqual(8, self.mut.stat(BamMutator.STAT_ALIGNMENT_MUT_COUNT))
bam2sam(self.RESOURCE_PATH + 'output_05.bam',
self.RESOURCE_PATH + 'output_05.sam')
self.assertTrue(
filecmp.cmp(self.RESOURCE_PATH + 'desired_05.sam',
self.RESOURCE_PATH + 'output_05.sam'))
def test_unmutate_07(self):
# include unmapped
with BdiffIO.from_text_file(self.RESOURCE_PATH +
'input.diff.txt') as bdiff_file:
self.mut.unmutate(bdiff_file=bdiff_file,
out_bam_filename=self.RESOURCE_PATH +
'output_07.bam',
unmapped_only=True)
self.assertEqual(4, self.mut.stat(BamMutator.STAT_ALIGNMENT_COUNT))
self.assertEqual(0, self.mut.stat(BamMutator.STAT_COVERING_COUNT))
self.assertEqual(0, self.mut.stat(BamMutator.STAT_MUT_COUNT))
# only the first diff record is read
self.assertEqual(1, self.mut.stat(BamMutator.STAT_DIFF_COUNT))
self.assertEqual(0, self.mut.stat(BamMutator.STAT_ALIGNMENT_MUT_COUNT))
bam2sam(self.RESOURCE_PATH + 'output_07.bam',
self.RESOURCE_PATH + 'output_07.sam')
self.assertTrue(
filecmp.cmp(self.RESOURCE_PATH + 'desired_07.sam',
self.RESOURCE_PATH + 'output_07.sam'))
def test_mask(self):
# EOF BAM case
Vac.text2vac(self.RESOURCE_PATH + 'input.vac.txt',
self.RESOURCE_PATH + 'input.vac')
bdiff_file = self._mut.mutate(
vac_filename=self.RESOURCE_PATH + 'input.vac',
mut_bam_filename=self.RESOURCE_PATH + 'output.bam',
secret=self.SECRET,
mut_p=0,
rng=self._rng)
cmn.bam2sam(self.RESOURCE_PATH + 'output.bam',
self.RESOURCE_PATH + 'output.sam')
BdiffIO.to_text_file(bdiff_file,
self.RESOURCE_PATH + 'output.diff.txt')
self.assertTrue(
filecmp.cmp(self.RESOURCE_PATH + 'desired.sam',
self.RESOURCE_PATH + 'output.sam'))
self.assertTrue(
filecmp.cmp(self.RESOURCE_PATH + 'desired.diff.txt',
self.RESOURCE_PATH + 'output.diff.txt'))
def test_unmutate_06(self):
# include unmapped with range
with BdiffIO.from_text_file(self.RESOURCE_PATH +
'input.diff.txt') as bdiff_file:
self.mut.unmutate(
bdiff_file=bdiff_file,
out_bam_filename=self.RESOURCE_PATH + 'output_06.bam',
start_ref_name='chr2',
start_ref_pos=1015, # inclusive
end_ref_name='chr2',
end_ref_pos=1028, # non-inclusive
include_unmapped=True)
self.assertEqual(13, self.mut.stat(BamMutator.STAT_ALIGNMENT_COUNT))
self.assertEqual(3, self.mut.stat(BamMutator.STAT_COVERING_COUNT))
self.assertEqual(2, self.mut.stat(BamMutator.STAT_MUT_COUNT))
self.assertEqual(1, self.mut.stat(BamMutator.STAT_DIFF_COUNT))
self.assertEqual(2, self.mut.stat(BamMutator.STAT_ALIGNMENT_MUT_COUNT))
bam2sam(self.RESOURCE_PATH + 'output_06.bam',
self.RESOURCE_PATH + 'output_06.sam')
self.assertTrue(
filecmp.cmp(self.RESOURCE_PATH + 'desired_06.sam',
self.RESOURCE_PATH + 'output_06.sam'))