def tearDownClass(cls):
global rvsrc, rvfd, rvsize
h = bs.munmap_binfile(rvsrc, rvfd, rvsize)
if h != 0:
assert False, "Error while closing the rsvk.10.bin memory-mapped file"
global vrsrc, vrfd, vrsize
h = bs.munmap_binfile(vrsrc, vrfd, vrsize)
if h != 0:
assert False, "Error while closing the vkrs.10.bin memory-mapped file"
def setup():
global mf
bs.munmap_binfile(mf)
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/genoref.bin")
mf, mfsize = bs.mmap_genoref_file(inputfile)
if mfsize <= 0:
assert False, "Unable to open the genoref.bin file"
def test_tearDown(self):
global rvmf, rvmc, rvnrows
h = bs.munmap_binfile(rvmf)
if h != 0:
assert False, "Error while closing the rsvk.10.bin memory-mapped file"
global vrmf, vrmc, vrnrows
h = bs.munmap_binfile(vrmf)
if h != 0:
assert False, "Error while closing the vkrs.10.bin memory-mapped file"
def setup():
global mf, mc, nrows
bs.munmap_binfile(mf)
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/nrvk.10.bin")
mf, mc, nrows = bs.mmap_nrvk_file(inputfile)
if nrows <= 0:
assert False, "Unable to open the nrvk.10.bin file"
def setup():
global src, fd, size, last
if fd >= 0:
pass
bs.munmap_binfile(src, fd, size)
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/test_data_col.bin")
src, fd, size, last = bs.mmap_binfile(inputfile)
if fd < 0 or size != 3765:
assert False, "Unable to open the file"
def setup():
global mfsrc, mffd, mfsize, mflast, idx
if mffd >= 0:
pass
bs.munmap_binfile(mfsrc, mffd, mfsize)
inputfile = os.path.realpath(
os.path.dirname(
os.path.realpath(__file__)) +
"/../../c/test/data/genoref.bin")
mfsrc, mffd, mfsize, mflast = bs.mmap_binfile(inputfile)
if mffd < 0:
assert False, "Unable to open the genoref.bin file"
idx = bs.load_genoref_index(mfsrc)
def test_tearDown(self):
global rvsrc, rvfd, rvsize
h = bs.munmap_binfile(rvsrc, rvfd, rvsize)
rvfd = -1
rvsize = 0
if h != 0:
assert False, "Error while closing the rsvk.10.bin memory-mapped file"
global vrsrc, vrfd, vrsize
h = bs.munmap_binfile(vrsrc, vrfd, vrsize)
vrfd = -1
vrsize = 0
if h != 0:
assert False, "Error while closing the vkrs.10.bin memory-mapped file"
def test_tearDown(self):
global mf
h = bs.munmap_binfile(mf)
mffd = -1
mfsize = 0
if h != 0:
assert False, "Error while closing the nrvk.10.bin memory-mapped file"
def test_col_tearDown(self):
global src, fd, size
h = bs.munmap_binfile(src, fd, size)
fd = -1
size = 0
if h != 0:
assert False, "Error while closing the memory-mapped file"
def test_tearDown(self):
global mfsrc, mffd, mfsize
h = bs.munmap_binfile(mfsrc, mffd, mfsize)
mffd = -1
mfsize = 0
if h != 0:
assert False, "Error while closing the genoref.bin memory-mapped file"
def setup():
global rvmf, rvmc, rvnrows
bs.munmap_binfile(rvmf)
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/rsvk.10.bin")
rvmf, rvmc, rvnrows = bs.mmap_rsvk_file(inputfile, [4, 8])
if rvnrows <= 0:
assert False, "Unable to open the rsvk.10.bin file"
global vrmf, vrmc, vrnrows
bs.munmap_binfile(vrmf)
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/vkrs.10.bin")
vrmf, vrmc, vrnrows = bs.mmap_vkrs_file(inputfile, [8, 4])
if vrnrows <= 0:
assert False, "Unable to open the vkrs.10.bin file"
def close(self):
"""Close all input files"""
if self.genoref_mf is not None:
pvk.munmap_binfile(self.genoref_mf)
if self.nrvk_mf is not None:
pvk.munmap_binfile(self.nrvk_mf)
if self.rsvk_mf is not None:
pvk.munmap_binfile(self.rsvk_mf)
if self.vkrs_mf is not None:
pvk.munmap_binfile(self.vkrs_mf)
def setup():
global rvsrc, rvfd, rvsize
if rvfd >= 0:
pass
bs.munmap_binfile(rvsrc, rvfd, rvsize)
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/rsvk.10.bin")
rvsrc, rvfd, rvsize, _ = bs.mmap_binfile(inputfile)
if rvfd < 0 or rvsize != 120:
assert False, "Unable to open the rsvk.10.bin file"
global vrsrc, vrfd, vrsize
if vrfd >= 0:
pass
bs.munmap_binfile(vrsrc, vrfd, vrsize)
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/vkrs.10.bin")
vrsrc, vrfd, vrsize, _ = bs.mmap_binfile(inputfile)
if vrfd < 0 or vrsize != 120:
assert False, "Unable to open the vkrs.10.bin file"
def test_tearDown(self):
global mf
h = bs.munmap_binfile(mf)
if h != 0:
assert False, "Error while closing the genoref.bin memory-mapped file"
def tearDownClass(cls):
global src, fd, size
h = bs.munmap_binfile(src, fd, size)
if h != 0:
assert False, "Error while closing the memory-mapped file"
vk.check_reference(mf, chrom=23, pos=0, ref='A')
# 0
vk.flip_allele(b'ATCGMKRYBVDHWSNatcgmkrybvdhwsn')
# b'TAGCKMYRVBHDWSNTAGCKMYRVBHDWSN'
# Normalize a variant - this function should be used before generating a new VariantKey
vk.normalize_variant(mf, chrom=13, pos=2, ref='CDE', alt='CFE')
# (48, 3, b'D', b'F', 1, 1)
# Return values are: code, POS, REF, ALT, REF length, ALT length
# Create normalized VariantKey
vk.normalized_variantkey(mf, chrom="13", pos=2, posindex=0, ref='CDE', alt='CFE')
# (7493989787586955617, 48)
vk.munmap_binfile(mf)
# /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\
# NRVK
# ----
# Load the lookup table for non-reversible variantkeys.
# The input binary files can be generated from a normalized VCF file using the resources/tools/nrvk.sh script.
# The VCF file can be normalized using the `resources/tools/vcfnorm.sh` script.
# This example uses the "c/test/data/nrvk.10.bin".
mf, mc, nrows = vk.mmap_nrvk_file('nrvk.10.bin')
if nrows <= 0:
assert False, "Unable to open the nrvk.10.bin file"
print(vk.get_genoref_seq(mfsrc, mfidx, chrom=23, pos=0))
# b'A'
print(vk.check_reference(mfsrc, mfidx, chrom=23, pos=0, ref='A'))
# 0
print(vk.flip_allele(b'ATCGMKRYBVDHWSNatcgmkrybvdhwsn'))
# b'TAGCKMYRVBHDWSNTAGCKMYRVBHDWSN'
# Normalize a variant - this function should be used before generating a new VariantKey
print(vk.normalize_variant(mfsrc, mfidx, chrom=13, pos=2, ref='CDE',
alt='CFE'))
# (48, 3, b'D', b'F', 1, 1)
# Return values are: code, POS, REF, ALT, REF length, ALT length
vk.munmap_binfile(mfsrc, mffd, mfsize)
# /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\
# NRVK
# ----
# Load the lookup table for non-reversible variantkeys.
# The input binary files can be generated from a normalized VCF file using the resources/tools/vkhexbin.sh script.
# The VCF file can be normalized using the `resources/tools/vcfnorm.sh` script.
# This example uses the "c/test/data/vknr.10.bin".
mfsrc, mffd, mfsize, mflast = vk.mmap_binfile('vknr.10.bin')
if mffd < 0:
assert False, "Unable to open the vknr.10.bin file"
print(vk.find_ref_alt_by_variantkey(mfsrc, mflast, vk=0x2000c3521f1c15ab))
def tearDownClass(cls):
global mf, mc, nrows
h = bs.munmap_binfile(mf)
if h != 0:
assert False, "Error while closing the nrvk.10.bin memory-mapped file"
def tearDownClass(cls):
global mfsrc, mffd, mfsize
h = bs.munmap_binfile(mfsrc, mffd, mfsize)
if h != 0:
assert False, "Error while closing the genoref.bin memory-mapped file"
