import re
from dae.annotation.annotatable import Annotatable
[docs]class Variant:
"""Provides variant defintion used in effect annotator."""
# pylint: disable=too-many-instance-attributes
def __init__(
self,
chrom=None,
position=None,
loc=None,
var=None,
ref=None,
alt=None,
length=None,
seq=None,
variant_type=None):
self.variant_type = None
self.length = None
self.reference = None
self.alternate = None
self.set_position(chrom, position, loc)
if variant_type in {
Annotatable.Type.LARGE_DUPLICATION,
Annotatable.Type.LARGE_DELETION}:
assert self.chromosome is not None
assert self.position is not None
if self.length is None:
assert length is not None
self.length = length
self.variant_type = variant_type
else:
self.set_ref_alt(var, ref, alt, length, seq, variant_type)
self.ref_position_last = self.position + len(self.reference)
self.corrected_ref_position_last = max(
self.position, self.ref_position_last - 1,
)
[docs] def set_position(self, chromosome, position, loc):
"""Set variant position."""
if position is not None:
assert chromosome is not None
assert loc is None
self.chromosome = chromosome
self.position = int(position)
if loc is not None:
assert chromosome is None
assert position is None
chrom, loc_position = loc.split(":")
self.chromosome = chrom
if "-" not in loc_position:
self.position = int(loc_position)
self.length = None
else:
start, end = loc_position.split("-")
self.position = int(start)
self.length = int(end) - self.position
assert self.chromosome is not None
assert self.position is not None
[docs] def set_ref_alt(self, var, ref, alt, _length, seq, _typ):
"""Set variant reference and alternative."""
if ref is not None:
assert alt is not None
assert var is None
# assert length is None
assert seq is None
self.reference = ref
self.alternate = alt
if var is not None:
assert ref is None
assert alt is None
# assert length is None
assert seq is None
self.set_ref_alt_from_variant(var)
self.trim_equal_ref_alt_parts()
assert self.reference is not None
assert self.alternate is not None
[docs] def trim_equal_ref_alt_parts(self):
"""Trim reference and alternative."""
start_index = -1
for i in range(min(len(self.reference), len(self.alternate))):
if self.reference[i] == self.alternate[i]:
start_index = i
else:
break
self.reference = self.reference[start_index + 1:]
self.alternate = self.alternate[start_index + 1:]
self.position += start_index + 1
[docs] def set_ref_alt_from_variant(self, var):
"""Set reference and alternative from CSHL variant."""
if var.startswith("complex"):
res = re.match(".*\\((.*)->(.*)\\)", var)
self.reference = res.group(1).upper()
self.alternate = res.group(2).upper()
return
var_type = var[0].upper()
if var_type == "S":
res = re.match(".*\\((.*)->(.*)\\)", var)
self.reference = res.group(1).upper()
self.alternate = res.group(2).upper()
return
if var_type == "D":
res = re.match(".*\\((.*)\\)", var)
self.reference = "0" * int(res.group(1))
self.alternate = ""
return
if var_type == "I":
res = re.match(".*\\((.*)\\)", var)
self.reference = ""
self.alternate = re.sub("[0-9]+", "", res.group(1).upper())
return
raise ValueError(f"Unknown variant!: {var}")