def setUpClass(cls):
global rvmf, rvmc, rvnrows
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 rvmmf, rvmmc, rvmnrows
inputfile = os.path.realpath(
os.path.dirname(os.path.realpath(__file__)) +
"/../../c/test/data/rsvk.m.10.bin")
rvmmf, rvmmc, rvmnrows = bs.mmap_rsvk_file(inputfile, [])
if rvmnrows <= 0:
assert False, "Unable to open the rsvk.m.10.bin file"
global vrmf, vrmc, vrnrows
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"
vk.get_variantkey_chrom_endpos(mc, vk=0x2000c3521f1c15ab)
# 1073841836
vk.munmap_binfile(mf)
# /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\
# RSIDVAR
# -------
# Load the lookup table for rsID to VariantKey.
# The input binary file can be generated using the resources/tools/rsvk.sh script.
# This example uses the "c/test/data/rsvk.10.bin".
mf, mc, nrows = vk.mmap_rsvk_file('rsvk.10.bin', [])
if nrows <= 0:
assert False, "Unable to open the rsvk.10.bin file"
vk.find_rv_variantkey_by_rsid(mc, 0, nrows, rsid=0X00000061)
# (9223656209074749440, 3)
vk.get_next_rv_variantkey_by_rsid(mc, 2, nrows, 0x00000061)
# (9223656209074749440, 3)
vk.munmap_binfile(mf)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Load the lookup table for rsID to VariantKey.
# The input binary file can be generated using the resources/tools/rsvk.sh script.
def __init__(self,
genoref_file=None,
nrvk_file=None,
rsvk_file=None,
vkrs_file=None):
"""Instantiate a new VariantKey object.
Load the support files if specified.
Parameters
----------
genoref_file : string
Name and path of the binary file containing the genome reference (fasta.bin).
This file can be generated from a FASTA file using the resources/tools/fastabin.sh script.
nrvk_file : string
Name and path of the binary file containing the non-reversible-VariantKey mapping (nrvk.bin).
This file can be generated from a normalized VCF file using the resources/tools/nrvk.sh script.
rsvk_file : string
Name and path of the binary file containing the rsID to VariantKey mapping (rsvk.bin).
This file can be generated using the resources/tools/rsvk.sh script.
vkrs_file : string
Name and path of the binary file containing the VariantKey to rsID mapping (vkrs.bin).
This file can be generated using the resources/tools/vkrs.sh script.
"""
self.genoref_mf = None
self.genoref_size = 0
self.nrvk_mf = None
self.nrvk_mc = None
self.nrvk_nrows = 0
self.rsvk_mf = None
self.rsvk_mc = None
self.rsvk_nrows = 0
self.vkrs_mf = None
self.vkrs_mc = None
self.vkrs_nrows = 0
if genoref_file is not None:
# Load the reference genome binary file.
self.genoref_mf, self.genoref_size = pvk.mmap_genoref_file(
genoref_file)
if self.genoref_size <= 0:
raise Exception('Unable to load the GENOREF file: {0}'.format(
genoref_file))
if nrvk_file is not None:
# Load the lookup table for non-reversible variantkeys.
self.nrvk_mf, self.nrvk_mc, self.nrvk_nrows = pvk.mmap_nrvk_file(
nrvk_file)
if self.nrvk_nrows <= 0:
raise Exception(
'Unable to load the NRVK file: {0}'.format(nrvk_file))
if rsvk_file is not None:
# Load the lookup table for rsID to VariantKey.
self.rsvk_mf, self.rsvk_mc, self.rsvk_nrows = pvk.mmap_rsvk_file(
rsvk_file, [4, 8])
if self.rsvk_nrows <= 0:
raise Exception(
'Unable to load the RSVK file: {0}'.format(rsvk_file))
if vkrs_file is not None:
# Load the lookup table for VariantKey ro rsID
self.vkrs_mf, self.vkrs_mc, self.vkrs_nrows = pvk.mmap_vkrs_file(
vkrs_file, [8, 4])
if self.vkrs_nrows <= 0:
raise Exception(
'Unable to load the VKRS file: {0}'.format(vkrs_file))